I am not a creator but I have some input I guess. It is very puzzling.
I edited Stericson's stock theme template, changed app icons (removed some apps) resigned each APK, modified the framework-res.apk (did not touch any xml files, and tried to only modify images I thought were changed to create Blue Star 5 - my basis for theming). I zipped it up, signed the zip. And updated my phone.
It took a while to get past the android logo (which by the way did not change color as I expected with the new framework files), but eventually booted up for me. No problem. My case may be special, because before I applied my update I removed some stock APK's and all the stock ringtones, ensuring I had room to spare on my /system partition. I removed amazon, email, and IM - the APK's and ODEX's. My update zip that I used initially to apply my theme contained :
All APK's except those listed above - resigned all that I modified.
And JUST the framework-res.apk
I have since modified some more files in the framework and created another update.zip that just included that file - it applied just fine.
However, no one else has been able to install this theme on their phone (that I know of), and I can't figure out why. Maybe it is the space that I had free?