It's best not to think of it as a "console port", this is a bit of a mis-conception. If you forget the ps3 version existed, you'll see that it's simply an excellent PC game.
I don't even know how we'd support the gamepad with Eden in its current form - perhaps you could move the jump targeting cursor around with the left stick or something? It would be a bit like playing an RTS with a gamepad.
I believe you that the mouse controls are far superior. It's just a pity that local multiplayer is now missing completely as a consequence of no controller support. I consider that one of the strongest features of the PS3 version, so it's a real shame that the PC version is now worse in that regard.