I've enjoyed every Yoshi game to date (including the puzzle ones), but Yoshi's Story was definitely the weakest of the bunch.
It could've been a lot better if Nintendo had made 2 changes:
1. Give each stage a goal - the fruit collecting should have been a bonus like red coins/stars in Yoshi's Island.
2. Let players play through EVERY STAGE in one play-through. I know that it was meant to increase replay value, but I didn't really care for the "6 stages and you're done" design.