I haven't played Elite Beat Agents, so I couldn't tell you there, but Hunters was almost universally hated for its control scheme. Didn't bother me all that much, but most people agree with you there.
For good ones... try The World Ends With You, Professor Layton, Civilization Revolution, or Final Fantasy XII: Revenant Wings. Off the top of my head. Most games it doesn't matter, though. Mystery Dungeon: Shiren the Wanderer, Contra 4, Scurge, Orcs & Elves, and similar either don't use it at all or don't rely on it.
I mean, it really is an unworthy prejudice, not because some games don't fail at it (like Hunters), but because for 90% of the games out there it just isn't an issue.