As I understand you talking about jquery and twitter bootstrap since only bootstrap code is splitted and has two versions.
Sorry about inconvinience but at this moment no recommended version choosen. So choose any and provide feedback on any problem.
I think bootstrap-related code will be merged in future so no matter what will be choosen, you'll help in any case.
If you want only jquery support then just use weblocks + weblocks-jquery
As for adaptation difficulties if you use much of prototype-dependent libraries then it should be difficult.