If it's okay for me to say, I think there's a way around your issue with omni in the current arc mha rise of ben 10 you're currently writing. That being to have MHA Rook keep MHA Ben at his low level of omni, and here's a few reasons why.
One reason is that MHA Ben is still too new at the hero business and still figuring out the omnitrix and it's aliens, so MHA Rook would feel that MHA Ben should focus more on mastering the omnitrix and maybe even stabilizing the ultimates more before moving on to the more advanced omni arts.
Another reason is that MHA Rook doesn't want MHA Ben to that strong that fast, and get an inflated ego. He knows easily arrogant MHA Ben could become from having that high a level of power this early on of being a hero, so MHA Rook has MHA Ben stay at his current level of Omni to keep him humble and until he's mature enogh to not become arrogant from that high a level of strength.
And the last reason could be because MHA Rook is too busy with teaching the rest of Class A omni arts. MHA Rook could want Class A to be better able stand on par with MHA Ben's aliens and have a better chance against the likes of the pack, alien Mercenaries, and the League of villains without having to rely on MHA Ben so heavily during fights, and maybe to use the omnikixs better without putting such a strain on MHA Ben.