As I said when you posted the first edition of this, I'm just not sure how both Bohemia and Royal Prussia are left out of an 'Germany united in 1848' scenario.
Honestly, I could see Bohemia being left out. It's a stretch, but I could see it. Prussia, though? Not a chance.
As I mentioned in the earlier post, by the time the Germans got together in Frankfurt to discuss union, Bohemia's independence from Austria had already organised. They were never on the table as being a part of Germany.
This Germany is a unification of the Deutsche Bund - barring Bohemia - and the excluded part of Prussia was never considered part of that until after 1848. Additionally, this union is, to an extent, being driven by the south, and particularly supported by Austria, so forcing their northern rivals to split their holdings is definitely on the table. The impetus for union is such that Prussia can't opt out, or else they'll face severe internal problems, so they accede to the Austrian demands and split their holdings. Now, this Prussia is majority German, and ruled by a German, so in the long term I can easily see them eventually joining - or they could go along OTL's Austrian route and develop an independent sense of nationhood. The map is only 1878, so it's not like the borders are fixed for all time.
AFAIK, the Sonderbund weren't trying to secede, they were trying to stop the federalisation of the Swiss cantons into a consolidated state. If they won the Swiss Civil War, the result wouldn't be them going independent, it'd be Switzerland remaining a loose confederacy.
While I agree that the Sonderbund weren't seeking independence, the Federal forces were pretty dedicated to their project, and I think that they would have continued along their centralising path. There's the additional splitting force that the Sonderbund here contains pretty much all the Catholics, and I think that'd be enough for de-facto separate nations.
Wouldn't Neuchâtel be returned to the Prussian King rather than annexed to a unified Confederacy or a confederate union?
Why? Neuchâtel essentially sat out the Sonderbund war, but its people favoured the Federalists, so I don't think it's out of the question for it to become a republic and join on a timeline roughly approximating ours.