Part of the reason that some of the GSC games may be wearing down faster than the RBY games might have to do with the greater toll that's put on the internal battery. In RBY, the only time the clock was used was when the game was on, so unless you literally had the game on all the time, it wouldn't run out that quickly. But in GSC, another internal clock measured the time even when the game was off (for the night and day as well as similar features), so it makes sense that it might run out quicker. The same may be true for RSE, since those games have a real-time clock as well.

This might be something that Nintendo should consider during the production of Diamond and Pearl. I would imagine losing all your data would frustrate a good number of people. Perhaps something like making the real-time clock optional would be a smart idea.