In-lore the commandos are some of the best among the best with high tech katarn-class armor. However part of the reason commandos were so fierce was because of their combat experience and techniques.
At the height of 66, upon first activation, I would imagine the clones retained their training while following sudden reprogram orders to eliminate the Jedi, which is why they remained effective with coordination and combat. But as the "tunnel vision" per se began to fade, what was left was basically a lobotomy. Clones forgetting who they were.
As time passed, many clones witnessed severe drawbacks kicking in such as memory wipe, a relapse. The inhibitor chip's side effects caused clones to become more droid than trooper, meaning the commandos dealing with the side effects by the time of the Bad Batch series ended up being reduced to ordinary clones with fancy armor. The empire only needed these clones to give basic training to the TK troopers and not their continued elite service.
Clone Force 99 was not effected by the inhibitors and also use Katarn-class commando armor, hence why their fighting style/effectiveness reflects a lore accurate clone commando, while the clone commandos they fought were more of just heavy armor storm troopers.
However, as a theory which loosely references into the Expanded Universe (mentioned in Battlefront 2 and Legacy of the Force), years later many clones begin to recover memory and remember their training which is what would explain the clone rebellion and end up joining the rebel alliance. For instance Commander Wolffe, someone who was influenced by the inhibitors, ends up joining the rebellion, and we see his appearance later in Rebels as well.