I agree that the certificate and profile thing is confusing when you are getting going, but I think a lot of that was exacerbated by not using the native toolse

I agree that the certificate and profile thing is confusing when you are getting going, but I think a lot of that was exacerbated by not using the native toolset. Xcode handles a lot of it for you (with more and better support coming in Xcode 5), and point you in the right direction for things you have to do alone. Plus, there is loads of help on the 'net about doing this stuff in Xcode because everyone has to, whereas PhoneGap's user base is lower, so less out there. I wouldn't say it's overly complex, but it is by no means simple.