My main problem with MUI is that folks write code that depends on various MUI classes that you then have to hunt down and install and sometimes the ownership of those things move, the websites change, the class ceases development, etc. etc. The lack of centralized ownership makes maintenance and installing a pain in the arse.
If MUI 3rd party MUI classes were simply licensed by developers that need them so that they could be iuncluded in the distro then that would help the end user and hopefully get rid of the 68k ppc compatibility problems that come up but setting up my MUI apps was a hassle.
With Reaction at least you know that all the UI componants are already installed.
As to the matter of portability, if your functionality is too closely tied to your UI engine then you are always going to have problems. If you separate out your function from the presentation sufficiently then porting from MUI to Reaction to Carbon to Windows to whatever should be much easier. It'll probably help keep your code more understandable too.
