Igniz has a very bad weakness that can be exploited by anybody who can possibly super jump over his head. He's still a boss in which most of his bar, if not all of his bar, can be taken down by a single character. There's only 1 character without the *ups* to do that jump, and that's K9999. He comes with his own baggage, though.
So Igniz is out because there's a fairly easy to execute, utilitarian way to beat him with every character.
I think the Magaki boss from XI is one of the hardest bosses ever. Though technically, Rugal has had a few doozies in there. Like '94. Mukai is pretty tough, too.
What works with Magaki, though, is that you are given more resources to put some real damage on him. The however is that it requires a new level of skill to pull off the best weapons on him. So he's tougher because he actually, in most character's cases, requires a higher level of player skill to pull off new and improved combinations, to beat him.
Other bosses usually die to good pattern matching and a few good damaging move landings whenever they're open. That is, you don't have to know any of the better-skilled combinations, in full. Just a few good damaging segments. So, in that case, it puts Magaki on a higher pedestal than most appearances. As usual, the command throw monsters (*ahem* Ralf, Clark, Goro, Tizoc) lose out in the lack of extra skill they need to beat a boss. One day, KOF will have a boss that gives them as much trouble.....One day.