I think that Marvel has the oppertunity to really make this guy into a great villian in the Ult. Universe, this is how I would do it if I was in charge at Marvel.

First, you do a 4-5 issue mini called Ultimate Doom. It picks up right after the FF's first fight with Doom. Hes lost everything - his followers, his "Kingdom" everything. He thinks about way's to kill Reed (robots, out smarting him, using his powers) and relize's that in each case Richards is better then he is and its driving him crazy, everything hes done and mastered, Richards had done better. Then he sees a magic show on the street and knows how he can kill Richads, by mastering something Richards doesn't even believe in. The rest of the mini would deal with Doom investing real magic, travelling the world looking for it and finally mastering it.

I would time the release of this mini. so that the last issue is shipped in the same month that current Ultimate vol. ships. The next month a big 6-8 month run on Ult. FF starts, one where Doom, using his new found powers, takes over his home country of Latveria. The Ultimate's (who's next vol. starts after this story arc) and FF go to stop him. However Doom win's the fight, and sends both teams packing, remaining in control of Latveria.

I dont know, I think we need the techy Dr.Doom before we see the unthinkable doom.

Heres my take

After loosing everything to richards, he decides that he wants the only think that reed will never have, and that is his humanity back. He knows the original formula and what was wrong, so he goes through the expeiriment and ends up fixing himself. Unfortuently the lone scar remains on his face from when Reed hit him in the last encounter. Show how vain he is and have him recreat the armor (exept in the actual armor) just to hide his face.

Personally, make the armor more along the lines of the 2099 armor. Kind of angular with some small spikes and the obvious green cape and yellow buckles. Lose the goat legs cuase he obviously wont have those anymore.

Personally have his relitives die of something, keep it open so you dont know if it was him or somethign else, and he takes the families fortune. With that fortune he has enough to fund his research and gain popularity Nation wide as a freedom fighter for his nation. Meanwhile have FF come back to find a way to be human again and they find him. Have him reveal that he is already normal and that they can go back anytime, just by using his machine (of course he is still armored and such, so he would just take them out afterwards). Reed, sue and storm fight with Doom and his new and imporved armor. Have Doom get the upperhand with hidden tricks like blasters and stun rays and such, while Thing walks closer to the machine and his humanity and body that where taken. As Doom presses the advatage agaisnt the 3, thing hurls the transforming platform at him and smashes both of them through a castle wall. They leave doom to due as he wishes cuase they can't bring him to justice and they can't become human as long as people like him are around. Show doom in anger at the end that Reed no longer wants his humanity and that doom is still scard and has been beaten again.

I may not pretend, aught rightly to know,
I may not pretend, through teaching, to find
A means to improve or convert mankind.
Then I have neither goods nor treasure,
No worldly honour, rank, or pleasure;
No dog in such fashion would longer live!
Therefore myself to magic I give [...]

Except it goes against what he thinks of himself. He LIKES that happened to him, hes not going to try to change back. And having hte magic/mystically powers is always made Doom cool - that he was both science and mystic.

He likes what happened, but he so wants to have things that Reed can't. And returning to normal is the only thing.

And he should get his magic eventually. But I feel it is to early for him to do that, ultimate wise atleast.