I've never made a 3d game before, so I can't say specifically how to make it feel better.
I wish I could give you exactly what it was that felt wrong, but it just felt like when I jumped I'd go further than I intended to, and I didn't have much control in the air to land where I wanted.
Giving it some thought. It might have had something to do with the character shadows. Check out "drop shadows" and how they help user experience, there are videos online about it. But it also could have been unintuitive momentum making me miss the platform. I did beat the game, but it was frustrating.