Sean,
There is another thread here that I was reading yesterday... it doesn't seem to be unique to you but the iPhone 4S in general.
I don't know why Apple decided to handle the battery charging in this fashion but then who ever knows why Apple does what they do. They make the N.S.A look like an open book library with their "Secretive Tweaks".
My guess is it is a designed in "Feature". One would think that the most effective method would be to charge to 100% and then turn off the charging and run from the charger module until it is unplugged thus leaving you with a 100% battery even if the phone was left on the charger for 24 hours (idle or in use).
L-ion Polymer batteries don't like to be fully charged and just left sitting for long periods of time with that battery at 100%. Assuming my comment is true you can find on the Apple support site a comment about the best way to take care of you iPhone battery is to "Keep the electrons moving" be it charging or discharging. (and while that is a bit of a paraphrase it is what they say).
I don't have a link to the other thread on this topic but I remember someone saying that the charger will not auto restart until you unplug/re-plug or the battery falls below 91% - but don't take my word for that little tid-bit.
PS - I was reading the other thread on this subject just yesterday so if you scroll down a bit it shouldn't be to hard to find.