For one thing the sticker mechanic just doesn't work with paper mario. What's the point of battling if you can't level up? You need stickers to fight, which you can buy, find, or get as rewards for defeatig enimies. But if you fight to get stickers, you will most likely lose more stickers then you gain.
The overworld map makes the game feel like it's split into levels, and that really takes away from the feel of being in a real breathing world. You only have one partner, but she doesn't help you in battle at all. But the story? Oh my god it is so awesome! Ahem. "Bowser has kidnapped princess peach so go save her mario in true rpg fashion!" I played through about half of the game before giving it up. There are no plot twists, no charecter development, nothing that makes you feel attached or care about the charecters or anything. After the original paper mario on the n64 and particularly the one on gamecube, the thousand year door, I expected more out of this title.