What about his FEET?
Damn it, I loved the Ultimate Doctor Doom Ennis introduced when he was writing UFF. Powerful, intimidating, bat-shit crazy, and highly distinct from his 616 counterpart. One of those points of distinction were his hoof-like feet; Reed even points them out as a marker of Doom's degeneration during their fight.
But as far as I know, that arc was the last time Doom had the hoof-feet. The next time he appeared, he was being drawn by Greg Land (guh) and looked exactly like 616 Doom. Did anyone, ever, take the time to explain this? Or was it just another case of an interesting idea being dropped entirely when the talented person writing it left it in the hands of the less-talented?