I just jumped into their irc channel to check if anyone had analyzed the reason for baksmali failing on the ICS odex files. It seems it was basically a function that had changed syntax, requiring several other changes but HomerSp sent me a working baksmali.jar. Smali then doesn't complain when compiling the result.
Unfortunately he went offline just after that so I'm not sure he would be ok with me posting it here so I won't. I'll write a script to deodex the files instead and upload the results if nobody else does so.
I was actually just curious about why it failed, didn't expect at working version just like that.
EDIT: Done and uploaded. Thanks again to HomerSp for the working baksmali.jar!
I just realized I forgot to fix the signatures so for the apps it will probably fail unless resigned. I leave that to someone else though. I have not verified that these are valid but as I said, at least smali didn't have a problem compiling them so they are hopefully ok.