AppMobi has a HUGE problem with published apps. It's not having a control over application version.
Have you contacted them about this? It does seem silly to have the AppMobi version instead of your app's version, but they may be willing to fix it.
Have you looked at Live Update as well? I think it's an autoupdate system for all your apps.
honeGap has also a HUGE problem. There's no sound support in construct phonegap builds (currently, I don't know if this is going to change - 
Ashley ? :) AppMobi has no problems with sounds.
I've tried, and failed, to get PhoneGap to play audio. It just doesn't support it AFAIK. AppMobi specifically provide an alternative way to play audio which I've plugged in to the Audio object, which is why it works. It would be nice if PhoneGap could play audio, but to be honest after a few months watching what they're doing and trying to prod them in to better supporting games, they just don't appear to be interested. I think they're more about supporting website-style apps. Their open source model also makes it hard to contact anyone in charge or get a clear status on what their plans are. I really like PhoneGap, but it's just not progressing fast enough. AppMobi are doing loads on the other hand, and things like playMobi look really good, which is why we're shifting focus - PhoneGap support is about as good as it can be right now.
n appmobi there's reading and writing contact data (exclamation mark here) required.
That's ridiculous for a game and is surely going to lose you players. I'll see if AppMobi provides a way to fix that, but you should contact AppMobi as well in case they can help you.
) appmobi builds have a com.company.company.appname package name for some reason (or maybe I didn't configure appmobi correctly)
I don't think you set it up right, I think it's supposed to use your project name which you set yourself to something like "com.scirra.spaceblaster".
) phonegap seems to be actually quicker than appmobi
There's no reason for either platform to be faster since they both use the phone's browser to display the game. So I doubt there is a significant practical difference. Hopefully directCanvas will help appMobi pull ahead.