Before a security update on 12/22/14 that brought back all my bluetooth issues I faithfully used the Apple Charger and Batteries ($30.00, Apple Store) for years. I would get the warning ONCE, acknowledge it and immediately check if I had a set in the charger in the kitchen. Once those charged (couple hours) I'd be set for quite a while. I used the same charger/set of batteries for years before I noticed my alert times were becoming more frequent. The batteries Apple supplies with the charger I think are Sanyo, very highly rated. But eventually they lose the ability to take and hold a long running charge. $30.00 gets you a new charger and 6 batteries. Not bad. I decided to get a brick of Duracell's at Sam's Club and they'd only last a couple weeks. I put them into my tv room remotes and would get a little bit more service out of them. I believe in my case the computer I use (a mid 2001 27 inch iMac) and the more recent bluetooth updates were not so compatible and the keyboard and trackpad were spending a lot of time and energy trying to ping the iMac. This is a machine I've owned since late 2011 and it was only after some of the recent software updates my battery issues appeared.
Good luck, I went back to a wired keyboard and mouse, no more weird glitches and software issues or battery usage since (3 weeks)...