I think Reed Richards to some degree makes sense as a villain. Based on the last issue, it seems that Reed has some pent-up rage and believes that his attempts to do science for good was only rewarded by pain and suffering. No one in his family or his schoolmates cared that he was a genius and instead was treated harshly (of course there is the blind spot of his mom and Ben Grimm actually being there for him, this can probably be used as a plot point later on if Reed ever gets back his conscience).
Most of his exploits in the UFF comic plus Ultimate Power backfired and he nearly ended the world several times accidentally (Cosmic Cube, the probe (he finds out it's not his fault but he was brutally punished before the revelation), opening their universe to the Marvel Zombies, luring the Silver Surfer and creating Van Damme as a villain making him indirectly responsible for Ultimatum). When he tried to help Sue in his own way post-Ultimatum, it was reciprocated by separation and he no longer works at the Baxter Building. This means that even if he had noble reasons and wanted to do science for good it seems that things never go well as planned. It can even be noted that he actually was able to one-up Doom in Frightful rather easily when they switched bodies and do a better job than Victor did.
He probably realized especially with how it was easy to outmatch Van Damme, that it is not Victor, but him who is the real Doctor Doom of the Ultimate Universe and he decides to embody it. This last one is just a thought and hope I might be right.
