Midoco,
I've not run into anything so far and have run 2 KickStarter campaigns off my printer. ...MakerWare has been a very reliable slicing program for us and didn't have a need to do anything to the MakerBot Replicator 2X beyond the thermocouples.

As for not being able to do things I thought I would be able too... I'd say that it was a bit of a surprise when I discovered what a hard time it was to print PLA with the 2X. ...Essentially what I found out whilst visiting MakerBot HQ and talking with the developers is that it was designed specifically for ABS and the venting and cooling systems aren't sufficient to keep PLA rigid before the feed motor tries to pull it into the extruder head. ...This results in snagging. ...For me however, I much prefer ABS printing over PLA. ABS is far more flexible and easier to modify in general. ...I was bummed though. I had bought a cache of PLA filament in my pre-2X excitement and now it's just sitting on standby.