If I understand correctly, the Nuncabola version is based on a recent trunk version, ie for example the new(est) replay mechanism is already implemented?
Yes. Replays should be compatible in both directions.
What exactly is the advantage over NB except for the timestep, are the libraries that you use now faster or do they have more features [...]
The advantages for end-users can be found in the list of changes posted above. If you don't mind the dependence on a JVM and the current lack of an installer, and can live with an English-only application, you may benefit from giving Nuncabola a try.
As for the libraries, I don't see any significant advantages (nor disadvantages, for that matter). One point worth mentioning is that Java offers a timer with better-than-millisecond precision which does make a difference. Another would be OpenAL's support for 3D positioning of audio sources. Though not used currently, I have some rough ideas how it could be employed in the future (think of associating sound effects with path corners, for example for the thwomps in mym's rainbow level).
[...] or differently asked, why didn't you just change the timestep and leave the rest as it was?
Adding interpolation to the timestep required splitting the solid data into a part that changes during the game, and a part that doesn't. This in turn required changes to many other parts of the program.
It was pretty much clear to me from the start that if I ever started serious work on the code, this would have to go along with turning the structure into something that appealed to me. There was no way I would spend my spare time fiddling around with the existing Unix-centric C codebase. Mind you, this may all come down to personal preference. While I did write stuff in C in the mid-90's, these days I prefer different approaches to developing software whenever available.
For low-level code, C still has a slight edge over Java (what with stack allocation of objects and const). However, most of Neverball consists of parts that I feel can be done better and more elegantly with high-level code such as the one Java allows you to write.
And, what were the reasons that you decided to release a "personal version" (whatever that is) [...]
"Personal" refers to the fact that in the end Nuncabola has, as rlk would say, a target audience of one: me. If more people find it useful –and I hope they do– that's great. That's why I made it public. However, in case some will say "Why didn't you implement X?", "I don't like change Y" or "This will never run on mobile phones!", the answer is, it's the way it is because that's what works best for me. Anyone is free to take the code and adapt it to his needs, just as I did.
[...] instead of, for example, proposing a patch that changed the behavior to your liking and asking for opinions?
Well, nothing prevents you from seeing the whole thing as an elaborate patch. And it looks like the opinions have already started coming in.
I'll reply to parasti's posts later.