So, the Omnitrix in this story is meant to be different from canon. Here's a small list of the powerups.
Prime Specimen/ Ambassador Survival Protocol- Azmuth originally created the Omnitrix so the wielder would be able to bring peace through the knowledge of the different species' behavior and instincts. A sort of Ultimate Ambassador. The problem? Extremist groups have been known to kill Ambassadors. The Ambassador needs something to increase their chances of survival, even if they don't fight.
This works with special gene-replication and gene-splicing technology made by Albedo and [REDACTED]. Why only change DNA when transformed? This alters the DNA of both the user's original form and transformations to add advantageous genes and rare mutations (regular mutations, not "I'm-a-freaking-crocodile-just-because" mutations- though this means different things for different species), allowing them to be far less than helpless even when they aren't a trained fighter. The User's true form shall be alterred over time, not instantaneously - that would be dangerous. Only pre-existing genes will register as able to be added. The Omnitrix will not be able to create new genetics(Mechrobe is an anomaly made by the Ultimatrix's somewhat buggy nature and the adaptation abilities of the chips). Azmuth has a special version of the mosquito-drones - redesigned by [REDACTED] - orbitting invisibly near each planet to scan the DNA of the species for new mutated genetics, allowing the DNA to be updated(Possible cheat: time travel to the future with mosquito-drone, scan the species, then bring it back. Have kids and jumpstart your species evolution a bit.). This also allows for more genetic diversity for the Species De-Extinction Protocol.
Example:
Tetramand Rockskin- Similar to the scales of a shark, punching a Rockskinner the wrong way will cut into even a fellow Tetramand's skin. Slightly incresed durability.
Tayden Bones - A Tetramand's bones are twice as durable as before.
Omnipendium - A feature unlocked by the first recalibration. Term coined by Cody. Teaches the history, biology, and culture of the species and their planet. Will make it a bit easier to figure out abilities.
Situational Activation - The Omnitrix will activate on its own to give the user the form most suited to handle a situation as to survive. Similar to canon, but without pushing the button.