If you're confident that you can predict everything your opponent will do before they do it, then go right ahead with the aerial choke, because unlike the grounded choke, there are no guaranteed followups. There ARE situational ones, though. For example, if certain characters, like fox, try to roll away from you after an aerial choke you can hold forward(important because every pixel literally counts) and down tilt and it will actually knock him out of the roll.
But since the opponent regains control of their character at the same time as (or possibly BEFORE) you do, the only think you're really safe doing is shielding.
The way that I see it is that the grounded choke is superior since not only do you have Guaranteed followups on the vast majority of the cast...and not only can some of these followups KO or lead into more attacks, but you're also free to try and predict what the opponent will do without the possibility of taking damage. On the other hand, aerial choke has no guaranteed followups and leave's you vulnerable from the moment you hit the ground. The only "safe" think you can do is shield since their getup attack will come out faster than you can jump, run, or do any of your attacks. Even if you could hit with a followup, it's nothing that you couldn't do more easily out of a grounded choke. It's like you're trading safety and guaranteed damage for the extra 2-4% that the aerial choke does...not a wise choice.
If somebody can check the startup times for the two moves, that would be great, but with my current knowledge they're the same (any difference is negligible). Wind down for the aerial MIGHT be less, but it's nothing spectacular or even noticeable, really. One benefit of the aerial choke was that it let you switch directions while running and choke backwards, but we've known for months(or at least I thought we did) that you can reverse the grounded choke in the same way.
Am I missing anything?