I've been having all sorts of battery issues too. Do you have a 1st Edition by any chance? If so, you may have that "voltage regulator" problem (or whatever it's called) like I suspect I do, and it is robbing you of some battery life.
That being said: I had an energizer 3 hour charger, and I wasn't getting more than 1 hour use out of my 2200-2500 mah batteries of various brands. I bought a Duracell 6 hour charger that came with some 2650mah batteries, still no improvement. I finally spent more and got a Sony 15min charger (which I believe is the same thing as what you have, just rebranded, but if not then they are still very similar) that came with 2500mah batteries. I get around 2-3 hours of use out of them with GnGeo running at 260mhz. If I run NES or MD games at 200mhz, I can last a lot longer. So you don't seem to be doing too bad.
The other thing I'll mention: these 15 min chargers don't seem to do as well with other batteries (as in, batteries of a different brand or different mah rating than the ones that were included). When I use my Duracell 2650s, my Energizer 2500s, or my Sony 2200s, I don't seem to get as much life as when I use the included 2500s. I think they have it figured out so it will completely charge the included batteries in 15 min. The instructions said that for different batteries, you need to leave it charging for an extra 10-20 min. Even when I do that, I still don't get as much time as when I use the included ones.