I think having cloak turn off if you're getting shot at is the most obvious change they should be making. If it didn't take 45 seconds to mark a cloaked person then maybe that wouldn't be as needed.
Yes, it should be like TSNE/C&D.
If you're using stealth whenever you shoot without a silencer it should be taken down, and if you get shot at it should be taken down as well. That's a reasonable way to balance it imo. Stealth outside of TSNE is such a silly idea anyway, even though I love playing the Infiltrator class. They also need to sort out the e.locators in this game, it lasts way too long compared to MGO2, plus there's skill that allows you to take more grenades/elocs. Every game now is just an e.locator spamming match.
Also why the heck does headshots take more than one bullet? it's like they want people to play with auto-aim/correction. Make headshots one bullet = kill, like MGO1 and MGO2. Then again the servers will probably last only a year this time so I don't think they really give a damn, they just want to sell as many MB coins as possible and then call it a day.
ed: And the gear selection is really weak. I honestly can't think of a single thing it does better than MGO2, not even <SONG> could save this game.