Having read this heated question about Unity vs. UDK vs. ID something, I'm curious to know: what the repeatedly-hit, most crippling limitation(s) of Unity?

In order to keep this question non-subjective, again, I'm talking about the top repeated offender(s) of Unity are. This is something that, as a Unity user, you really wish someone had told you about before you started using it.

I have heard from someone that Unity does not deal well with version control, since it generates a lot of binary files (which are un-diffable). This, to me, is not really crippling as I work alone.

Thoughts?