Not so hard. James VI after his Spanish Match for Charles I crashed and burned so spectacularly, was angling for an Austrian archduchess/Spanish infanta for his eldest grandson. Several times during the 30YW the Habsburgs tried to get Prince Rupert onside by attempting to get him to convert to Catholicism. And after the 30YW, both the Winter Queen and Ferdinand III (at different times) attempted to broker a match between an Austrian archduchess (Maria Leopoldina, OTL Holy Roman Empress) and Karl I. So Friedrich might end up married to Cecilia Renata/Maria Eugenia (the archduchess/infanta alive at the time of the marriage negotiations) or Cecilia Renata (who married pretty late OTL)/Maria Leopoldina. And an interesting spanner in the works might be Cecilia Renata marrying Friedrich VI/Karl I, while the Winter Queen's daughter, Elisabeth, marries King Wladyslaw IV of Poland as was originally suggested (Wlad thought a Protestant wife might ease his succession in Sweden over the child Kristina, and talks were dropped thereafter).
Again what makes the Habsburgs WANT to restore the Palatinate to the Winter King or his heirs? Just because the Stuarts wanted a Habsburg-Palatinate match doesn't mean that the Habsburgs wanted one. In this TTL the Emperor has won the war, the rebels and the Danes have been crushed, the Swedes and the French aren't at liberty to intervene and the English have no real influence to use to push for a restoration. Maybe a Catholic Friedrich VI could get the upper Palatinate like his brother did OTL, but it would remain under occupation, wouldn't get a new Electoral title and probably wouldn't get an Archduchess. Though, if Ferdinand II has a daughter or two with his second wife, maybe and I mean maybe, she could be married to the Count Palatine of the Rhine. But still pretty unlikely.
What allows the Commonwealth to rally and what stops the Russians from joining Sweden and Brandenburg at this point when the PLC is at its weakest? If you can find a good explanation for those two questions I think the scenario would be plausible. In regards to a full counter-reformation, I think it is highly unlikely when you take into account that for Saxony and Brandenburg to go through with supporting the Emperor, the religious aspect of the conflict has to be minimized as much as possible. The Bohemian revolt was about the usurpation of a throne and general treason against the empire, not a religious rebellion supported by co-religionists against a heretic oppressor. I can see both the Wettins and Hohenzollern converting to Catholicism, but I can't see them ever going through with a counter-reformation, would be far too expensive and dangerous for the rulers.
Not sure of the how just yet, I'll have to research it further. Maybe the Imperial intervention in the Swedish-Polish war goes better? IDK. As for the counter-reformation, I agree that Saxony is likely out (as the birthplace of Lutheranism it would take a massive Catholic occupation and colonization to even begin to re-catholicize the Electorate) but am not sold on Brandenburg. The Margraviate had the smallest population of the secular Electorates (around 360,000), so it would be the likeliest to be converted, or at least gain a sizable minority. As to the religious aspect, its still quite minimized. This scenario would have Brandenburg's conversion as a result of losses outside of the Empire and a need to gain the support of the ascending Catholics. More political than religious.
I think we might see the Queen of France start trying to promote some of her supporters after Richelieu's fall, and I don't think she would allow Richelieu the opportunity to return to grace. Once he falls his numerous enemies would turn on him quickly. You might see Anne of Austria and Louis XIII grow closer once more, with a child born earlier than Louis XIV was. Without Richelieu the rift in their marriage might repair earlier than IOTL. Are there any notable supporters of Anne at this time who could replace Richelieu as Chief Minister? With a weakened and distracted France, could we see the Bourbons capitulate to Habsburg dominance of Europe, promoted by Queen Anne and her favorites? This might allow France some external support against the ascendant Huguenots and might very well end up being viewed as an extension of The Wars of Religion. Another direction for all this might go is that the Huguenots could begin to play a larger role at court as they did at various times during the Wars of Religion. There are so many different layers to the changes all this brings to France that it is hard to get a proper idea of what might happen.
The only way for Anne to have any influence is if she has a son earlier than OTL. Childless Queens can't expect to exercise much patronage or have much importance. As for favorites, hard to say. Anne's long childlessness meant that nobles didn't really rally around her OTL, but she was close to the Marie de Rohan, so her favorites would likely include the Rohan family, Marie's second husband the Duc de Chevreuse and Marie's circle.We might also see some of the high nobility support her if Louis XIII continues to invest power in a single favorite. As for Bourbon capitulation, not likely long-term but possible in the short term, especially if the French really need Habsburg support in dealing with the Huguenots. I think we'd still see a Franco-Spanish war break out, see France try to displace Spanish influence in Italy, continue to support the Dutch and try to get Bavaria to block Habsburg influence in the Empire.
Hell here Bavaria could end up acting as TTL's Sweden, a back door way for the French to challenge the Habsburg supremacy. Could be a way to destroy the Catholic League as well and a way for the Palatinate to get back to the Winter King's heirs. Not entirely sure if that's likely though. At the least they wouldn't get French troops but maybe French money. Also, it could be interesting if the Huguenots could be co-opted into the French government and military.
I don't think by this point in time that the Netherlands are ever going to be part of Spain again. The Spanish retaking Zeelandic Flanders and reviving Antwerp seems far more plausible and would allow you to work with a more equal split in power between the Northern and Southern Netherlands. I don't think the north would be completely crippled by a reopened Scheldt river, but it seems more likely to me that the two would end up competing actively against each other in trade as well as war.
As for Mantua, I think what you are proposing would work out well. One thing to take into consideration is that Cardinal Mazarin only really moved into the French camp during the negotiations surrounding the War of Mantuan Succession. What I was wondering was: What if Mazarin ends up working for the Habsburgs? Mazarin might be sent into the HRE to support an expansion of the Counter-Reformation and come to the attention of the Habsburgs there. Without the War of Mantuan Succession to bring him into Pope Urban's orbit, he might very well move to support the Habsburgs. Pope Urban was impressed by his martial abilities IOTL, and if you look closely at his leadership of France during the regency and through the creation of the Treaty of Westphalia, Mazarin was a powerhouse of the time. Richelieu is often held up as superior, but Mazarin should be considered a very close second. With Mazarin working for the Habsburgs you get the sort of expertise and ability that is largely lacking among the Imperials (well not lacking, but you don't have any of the powerhouses that the French/Swedes had in Richelieu, Mazarin and Oxenstierna).
By this point in time you could see the Habsburgs sponsoring him for Cardinalship, and an eventual position as Pope (unless I am very far off my mark here, I am not too clear in my knowledge of Papal history). This also leaves the question of changed circumstances for Mazarin's nieces, who could end up married into any number of families further changing up things.
The Dutch situation is one of the hardest to deal with, at least in my opinion. The better the Spanish do, the more the idea sets in that " hey we've conquered this much, maybe we can take the whole thing!". I have seen a Spanish conquest kind of done once, though I'm reluctant to suggest it. The 1632 series (quite cool books involving a time-traveling American town sent into the middle of Thirty Years' war Germany) has the Dutch fleet destroyed by am Anglo-French-Spanish force and the Spanish land troops behind the main Dutch defenses. Now this is very unlikely to happen without the ASB in 1632, but it is theoretically possible. So for now I'm not willing to completely dismiss it. At the least I think we'd see the Generality Lands be restored to Spain. Could counterbalance potential loses to France, like the County of Artois or the Archbishopric of Cambrai. Something else to consider is a reopened Antwerp could mean the establishment of a Northern Spanish fleet capable of rivaling the English, French, Danish and Dutch fleets, especially if an Imperial navy is also established in the North and Baltic seas.
Funny enough I had also considered a Habsburg Mazarin. We could still have a short Mantuan war, but instead Mazarin sides with the Imperialists over the French/Mantua. Here he becomes Vice-Legate and later Nuncio to someplace in the Empire and enters the service of the Emperor, eventually becoming Chief Minister, probably under Ferdinand III (doubt he would be able to become Pope if he's to closely associated with the Habsburgs: France would veto him). Here Mazarin's nieces are likely to instead marry into the cream of the Habsburg nobility: think families like the Houses of Hohenlohe, Clary und Aldringen, Auersperg, Croÿ, Lobkowicz, Lichnowsky, Dietrichstein
and maybe the Thurn und Taxis. They wouldn't be able to marry into the reigning Princely dynasties because they wouldn't be equal matches.
I think your description of the situation is very apt. The Habsburgs have an incredible opportunity to strengthen their grip on the HRE in a way not seen since the Hohenstaufens. I doubt a ban on armed forces would be possible this quickly, but setting limitations on military forces should definitely be possible. a ban on alliances with foreign powers should probably also be possible. It is internal leagues/alliances that I think are going to be the most challenging part to achieve and likely not possible right after the Catholic League has proven itself so successful. The centralizing process would probably be a slower process with specific rights having to be chipped away bit-by-bit.
Basically the Holy Roman Empire is being transformed from a medieval federation of feudal hierarchies into a centralizing early modern nation-state. While an outright ban on private armies is unlikely, I think strict limitations are possible, maybe an upwards ban of anything over 5,000 or so for the Electoral states. As to the leagues, I included an idea that has Bavaria, backed by France, try to challenge the Emperor's power and getting stuck down. That would discredit the German League and allow for its dissolution. I also think we could see some new institutions be created, like departments/ministries for taxation, war and foreign affairs. Under different names obviously, but definite emergence of state institutions and bureaucracy. Some taxes would end up either permanent or for life to help support the new institutions and the standing army. Here there is a definitive foreign threat, proved by Denmark and alluded to by France and Sweden.
I'm also considering a more revived role for the Imperial circles, like transforming them into something more in line with Provinces and appointing imperial Governor-Generals/Directors to each. At this point the next thing to consider is Hungary. With the Emperor fully focused on Germany and soon to be ruling an actual Empire, would he cede the Hungarian Crown to a second son or would he keep it in personal union? And what happens if/when the Turks begin to be pushed back? We'd have a Monarchy spanning from the Balkans to the North sea. Clearly such a stage would be next to ungovernable, especially as Hungary would lay entirely outside of the Empire.
Finally, I just got
The Thirty Years War: Europe's Tragedy by Peter L. Wilson, which seems to be an excellent source. So I'll probably post more as I delve into it.