Well, I can see how isometric games can be confusing. If you take a game like Lock's Quest for example (awesome BTW), there are times were you wish you had a camera to change the view of. Like if you need to do something behind a tall structure, there's only so much you can do effectively since you can't see your character (even if they make a shadow). It varies from game to game of course, and person to person, but I think the main disadvantage to that style is that the characters can't always be seen too clearly.
And of course for a thing like a tactics game, it's largely...
OpenGL supports sprites, and the new DirectX does, too, in an awkward way. There's a lot that can be done with pixel art in three-dimensional space. I'm surprised nothing has followed the technical feats of Yoshi's Island.