I don't remember where I read that he reserves the side arm for those enemies who aren't worth of getting a shot for one of the power beams of his suit.
And yes Doom should have some variety on him, I mean he is royalty after all, he can afford it. About the Ultimate universe was very sad, the Universe started all promising and interesting but after Ultimatum all the character developments and histories gets all messed up and wasted. Nowadays there are very few thing worth of rescue in that universe and certainly that Doom is not one of those having a much more interesting one in 616.