So a german centralised kingdom with no protestant principalities able to opose to Habsburgs in their quest to have what french kings achieved.
Basically erase Prusia from history.
Erasing Prussia (as we know it) is quite easy at such an early stage.
Don't forget that the fiercest enemy to what French kings had achieved were not only Protestants, but Bavaria.
Actually, I'd say Bavaria was the biggest obstacle for Ferdinand in his hereditary plans.
Therefore, Bavaria (and other insubordinate Catholic principalities, like Palatinate-Neuburg) are natural collaborators with France.
Go figure how Austria can win a war against them which in reality they lost with them at their side ...
They quickly win versus Boemian nobility.
They make a compromise to keep the religion and the Habsburg keeps the crown.
Why should they grant religious freedom?
That's a big constraint in the power of a monarch, even "as French kings had achieved".
Anyway, this already makes clear that you need a different personality in Ferdinand II. at least, if not a completely different trend in thinking.
Now why would Danmark and others still come in? well ...
Because they still have power interests?
Don't believe the fliers of 400 years ago that the war was about religion ...
Well, and concerning freedom of religion of the princes and of the people, there were quite a lot of triggers of conflict in the Northern half of Germany (Magdeburg, Halberstadt, Bremen, Oldenburg, ...)
Or we can make Sweden defeated by Poland, the king dies...
You mean Gustav Adolphus falls in Poland?
That's quite possible, given his courage in combination with his myopia ...
And it would definitely create a major change in the course of events. This is worth pursuing!
The crucial question is whether without him, Sweden would still intervene in Germany. I would tend to say "no", as this was a really venturesome plan. However, remember how smoothly Sweden could continue the war after his actual death.
North german protestantism survive as religios comunity but the princes lose they status.
They are replaced with protestant guvernors.
I don't understand that completely.
You want to deprive of the princes their right to be Protestants, which they had been acknowledged already a century before by the Emperor and the other princes?
Or you want to dispossess them of
their hereditary claims, which are beyond doubt?
This sounds completely revolutionary, even more than the Emperor's actual plans (like re-sacralization of bishoprics which had long been incorporated into Protestant principalities). This rather seems to be the project "how to turn a Thirty Years War into a Sixty Years War" ...
More to the point, I think the Emperor cannot
win over all princes at a time.
And of course, the princes are not stupid; they understand what the Emperor may be up to. So he cannot deal with them "in a row".
I can only see princes letting privileges "slip away", or give them away while they need support in more serious conflicts. You won't achieve a completely centralist Empire by 1650 with a PoD in 1618; this requires a bit more patience.
It seems possible that we can get on that track though; but I think that the Emperor will need the support of some of the princes. In particular, I think Austria cannot do much better than IOTL without an alliance with the Elector of Saxony in the short run.
In the long run, there cannot be an Empire completely under Catholic rule (and a couple of Protestant cities - don't forget them!). Whether the Emperor or the Princes or some Diet will have the power in their hands, they have to deal with different creeds - and I also think it's to late to prevent Calvinist princes by force or by law.
France tries to change the tides but gets owned on battlefield.
One suggestion: France was occupied with internal problems for a long time (Hugenots ...).
Once they start turning their attention to the East, they might be satisfied if they can expand their influence in Northern Italy by far (in addition to minor border corrections in Lotharingia, of course). In that case, they would not necessarily enter the war.
You would then have to deteriorate France's internal problems and change the complications in Italy (a different "War of Mantuan Succession").
The most important point, however, would be to keep the Emperor too busy to do much against France in Italy. IOTL, he intervened although he couldn't really afford that ...
Netherland-Holland would still gain independence because they are under spanish line of Habsburgs but maybe a bit later?
You want a split in the Habsburg family?
That sounds somewhat promising for your goals as well.
IOTL, the two Habsburg branches didn't always have interest aligned to one another, but they almost always agreed on some joint policy. This is because they thought of themselves as rulers with a claim to universal power in Europe which could but be achieved together.
If there is a serious split between these two families (one bad person doesn't suffice!) this might inspire the Emperor to pursue more realistic goals, and perhaps focus on the Empire proper. IOTL it weakened the Emperor considerably that he engaged in areas with Spanish influence (Netherlands, Milan).
However, even if the rulers of the Netherlands are completely unrelated to the Emperor, he would still be in the disagreeable situation that he would have to enforce allegiance from the Lord of that country; and in particular, he would have to take sides who he understands as that. In addition, without Spain Austria will lack a strong defender of the Rhineland against the revolutionary Netherlands, as well as France.
Just a couple of comments to your suggestions.
You take your pick ...
