Agreeing with a lot of poings on here, but I'm actually okay with the nazi allegory(even if it was a bit underdeveloped).
More aliens, by which I mean more IMAGINATIVE aliens. A lot of Ben's newer aliens were pretty much just different variants of his previous ones, Jury Rig was basically Grey Matter with personality, Swampfire is Heatblast/Wildvine with the saddest voice possible, and Walkatrout was Ripjaws if it just gave up on LIFE! More Pesky Dusts and Molestaches, especially the latter as that super mustache was AWESOME!
Properly utilizing Clockwerk. Seriously, this was probably Ben's most useful alien...and he almost always screwed up using him.
Lax main villains who are Ben's aliens. Side-villains sure, but honestly Dr.Psychobos and Maltruent were never big in terms of main villains to me, ESPECIALLY Maltruent. Its weird because I actually liked the arch he was in, but honestly felt Maltruent to be the weakest part, and his only real reason to exist was to explain where Vilgax got the time bomb! Speaking of which-
-make Vilgax the main villain from beginning to finish. Omniverse made the mistake of NOT doing this by killing him off after doing the fusion dance with Malware's corpse- IN A STANDALONE EPISODE! Not the series finale, a stand alone! What?! Omniverse I love ya, but come on!
And finally- KEEP THE ORIGINAL DESIGN! Stop fixing what isn't broken, LOOKING AT YOU OMNIVERSE OMNITRIX! Plus that slidey deal seeme pointless.