I know that the Commander is based off the TA one and it already has the Uber cannon, but will it have the cloaking and radar invisibility that the TA one did?
The commander didn't have radar jamming in TA, just a cloak. I imagine something like that will be possible, since they are going to have each commander have a different loadout of abilities. A stealth suite seems like a shoo-in for that sort of thing.
While the TA Commander did not have stealth, TA radar was so weak that it didn't really matter. Cloak/Stealth is a really good ability for Commanders to have. It'll be strange to find one that succeeds without it.
