Hi,
For what it's worth my degree is CIS, with years of professional experience troubleshooting network and PC issues, mostly on the software side though.
I've never had these issues with Apple products before and have less experience troubleshooting them. This is just personal perception and guesswork for me. I did not take advantage of the tools and dump logs made available more than a casual glance. I just changed carriers and upgraded my phone, half frustration and desperation, half lack of time to mess with this, laziness and been thinking of upgrading phone and service anyway.
So, I think the whole charge cycle advice is real, but software based. It seems to have helped many, and it did me. I also did a hard reset right after though. I took the shotgun approach and things improved greatly.
I think my issues were tied to buggy software and out of control cell data usage.
My first problem after upgrading was my battery life dropped 30-40% about, and dropped faster when using Safari, especially pages with heavy JavaScript and auto refreshes and key logging on input boxes it seemed.
After following almost all advice here, including discharge, recharge, reboot, things improved drastically.
Then I started using iTunes U. I tried to only download tutorials when on good wifi, put iTunes specific cell data to off, and would get messages when I left saying it could not download them over cell data when leaving wifi, so I thought that couldn't be it...
My phone heated like crazy and burned through my entire shared plan in days. I desperately had to turn cell data completely off, crippling my phone since the culprit ignored all iTunes settings to restrict to wifi. My phone wouldn't register the cell usage my carrier was telling me I was using up. Both phones, 4 and 5, different carriers seemed to behave the same shortly after trying to download iTunes U tutorials over wifi.
Also, after 6.01, iTunes Match seemed to suck battery and data even on playlists I had conscientiously downloaded from wifi first...
I look forward to Apple adding true battery and cell data logging on an app by app basis, and including their own apps in that user level of logging and control, so I'm hoping they do just that. It was great not needing those tools when things "just worked". It seems like they're trying to add some of the cloud and multitask features that made android popular, but forgot all the mess it caused with out of control data and battery before android added more user level monitoring tools and refinements.