Honestly, I just wouldn't have included a reason for Sora to become weaker, but would let the game play out the same. How much stronger Sora grows in each game isn't even very quantifiable. When you get to the end-game enemies, lots of them are just the same old ones with higher stats, so their and Sora's increase in strength might have just been for the sake of gameplay. Of course that doesn't account for lost skills, but hey, they didn't even bother explaining why Terra and Aqua only had a few skills at the start of BBS, and it wasn't a big deal there.
Thinking about it, I actually don't have a big problem with most of the explanations for Sora's de-leveling. But the explanation they gave in KH2 was just awful. "You slept for a year, you're out of practice." Give me a break. Sleeping for a year, especially in a stasis pod that seems to eliminate any need for food or water, should not erase all the progress you've made. My lifestyle is largely sedentary right now, but I still have a lot of the muscle that I built up 2 years ago. And I didn't have to fight monsters on hourly basis to get that muscle. And what, do wizards constantly have to practice magic in the KH-verse or else lose it completely? I guess I'll have to take that for granted, nothing outside of this excuse for de-levling even suggests that.