This bug has been driving me nuts for so long. Both ways of creating new files in AppCode have problems:
1) Using "New -> File from Xcode Template" creates files that leave the __MyCompanyName__ field unexpanded.
2) Using "New -> Class" uses file templates that don't have enough variables in them to use them as an identical replacement for the Xcode templates.
I've been following various EAP tickets related to performance (which you guys are doing a fantastic job at addressing!) and I remember seeing a question from someone at JB wondering why people still create files in Xcode rather than AppCode. I tried to find that comment and leave my answer, but I couldn't find it again. So anyway, these two file template bugs are exactly why I have to use Xcode to create files and thus unnecessarily cause AppCode to reload the project over and over again.
If you fixed either of these simple problems, I'd be able to stay away from Xcode even more (which would be great!). BTW, if I didn't have AppCode I'd probably quit iOS development so keep up the amazing work!