I'd make it able to create it's own alien with a selection and/or AI. For the AI part, if the Omnitrix saw, for example a fire, it would instantlytransform Ben into a alien with hydro powers, and also slow down time for Ben so that he could formulate a plan (he speed is still slowed down, just his cognitive functions are increased). For the selection part, the Omnitrix can combine DNA to form a mutant. For example if there is a large scale threat on the other side of the universe, Ben can combine Toku'Star DNA, Sonorosian DNA, and Aerophibian DNA, to form a mutant that retains the full powers of each alien.
I'd make it able to use the Ultimate features, but without the drawbacks. Master Control would only be auto unlocked if it's neccesary, and I'd make it able to scan mutants, Ghosts, E.V.O.s, and allow the wielder to turn their limbs into an alien's limbs, as well as the idea that the aliens could have ghost abilities.
Design wise it would look like an upside down Xtransceiver, from the Pokemon franchise, but with Purple accents and more of a smart watch theme/feel.
Features/Gimmicks was very complicated to figure out as most ideas were either repetitive or one off ideas that didn't stick. I did come up with a gimmick that felt unique that I actually liked and it was Tattoo mode; basically the Omnitrix would merge itself with the skin or skin equivalent of the user/transformation and take on the appearance of a tattoo and have the ability to revert to normal. The style of the tattoo would vary based on Omnitrix placement and species. Other tattoo mode there's no other feature/gimmick worth mentioning and are just repeats of the Omnitrix can already do