I had the following experience with Apple support.
I contacted them via twitter, not really to get a solution but trying to make them more aware of the problem.
The technician ran some remote tests on my phone, said that it was ok.
Asked me to reset the phone and then restore a backup, this is interesting because in the Genius bar they had told me to not restore the back (which I did). I explained to the technician that I had done that already to no avail.
So he had a senior support person contacting me on the phone. He asked me some questions but when I mentioned that I thought the problem was with iOS he just changed the topic. He didn't say no, it's not iOS or we don't know, he simply ignore it which somehow tells me Apple has told them not to say anything.
He recommended me to go to the Genius bar again and check the phone again, and maybe replace the battery, but he made it clear I would have to pay for it since I am not under warranty, I told him that I wouldn't have a problem paying to have my battery replaced IF it would solve the problem, but two different tests showed the battery doesn't need replacement and I know some people did it but the problem didn't go away.
I am certain it's iOS and I strongly suspect it has something to do with the GPS. If I am running a battery draining app that doesn't use GPS (e.g. videos) it doesn't drop, but if I am running a gps enabled app, it does when it reaches certain thresholds, and now it's getting worse, dropping from 50% to 1%, then back to 50 as soon as I plug it in, I have to have a battery charger with me all the time and this is getting really frustrating.