Hard mode Nintendo games? No substance, no difficulty. Nintendo have always made casual games. I think you're talking about Bethesda or pre-Dragon Age Bioware.
It's gotta be BC, though I did get a blast out of (I believe it was) Armada. There was this junkyard map where you could pluck some ships to add to your cause, including a borg cube (Though I may have cheated that one in, can't remember after all these years). There was another back in the days of the PowerPC with a top-down perspective, not official of course, but trying to answer Q without annoying him was a good challenge. There hasn't really been that many that stand out, come to think of it.
If/when the oh-so-fittingly named E comes out, I guess my mind'll change, but until then, BC keeps my vote.