the plan is to keep MB3 named as MusicBee3.exe
MB3 already has its own settings file
Whether you maintain backwards compatible skins is your choice ( i would suggest there is no need to support the removed 2.5 features as long as you make clear its only for v3)
The main reason is i am expecting a small and vocal number of people to say they hate it, or complain about feature xyz not being exactly the same - so this makes it easy for them to go back to 2.5
I've thought about this, but it doesn't make much sense.
Why is the transition from v2.5 to v3 so different from previous ones? When people didn't like a new version, they always just stayed with old versions, understanding there won't be any support for those. And I saw some still using v2.1 in the forum. I just checked the latest version forum and still all version since v2.1 are downloadable. So if people decide not to upgrade to v3, they can just stay.
Including v2.5 in the v3 installer, and even in the filename MusicBee.exe (not MusicBee2.exe), gives an impression that you're gonna keep maintaining that version along with v3 like adding new features to both versions and fixing bugs. Is that your plan? If not, why not just drop v2.5 like previous versions?
This already starts creating complications, notably in skinning. For the compatibility (even though it's optional) skinners have to abandon or compromise in many areas.
Hope you reconsider this. No one would complain about that as long as old versions are available.