they could get pretty annoying in your first playthrough (Which may be your last if you can't get over them), it's one of those kinds of controls that work when you're not thinking about them, but the moment you need to concentrate, you fuck up because how weird they are.
Which is sad because the game itself is pretty good and a classic of the Genesis (Although some of the latter places have some bullshit moments).
Besides the d-pad, the only bad part is the non-existent shadow, which I find vital for isometric games, as PresidentLeever comments...