Some people like to play a game where they overlevel or grind a lot. Just because you do doesn't take the fun away. Some people don't always enjoy a challenge, but love the feeling of being an unbeatable protagonist in a game (which would require grinding). So I wouldn't always so that when you overlevel it isn't fun as it could be. Honestly, depending on the game, I find it much more fun to grind in some than just go through the challenge (for example, I find grinding in FFXIII and Pokemon much more fun than just struggling over and over...I even tried it in Days and discovered I had the same amount of fun as usual in KH games)
The problem with that is then people would ask why you couldn't fly from area to area, completely avoiding the need to fight enemies or take the boat to Skull Rock, or even get hit by the cannonballs by Hook's ship. In KH1, you were in a ship, so you could only go so high in the rooms you were in as they had a ceiling...the ship exterior though felt awkward sometimes as I didn't understand why Sora couldn't just fly over to the island...it didn't make much sense to me...so I think they tried to avoid the player feeling boxed in.