EX Upball whiffing actually seems like quite a boon on wakeup for Commando, as his buffs in general did. I actually believe Commando to be a lot better than the bills being sold.
Think about it this way; you now have a safe wakeup that the ONLY way to really avoid is to crouch at a certain distance. Now that's dandy against the other two variations, but Commando's grabs do a great job of regulating that space to where if you just wait and crouch for it, you will likely get grabbed. I don't doubt there's a certain amount of low profile things that may beat both, but that's life.
Either way, this makes Kano's far trickier to pressure, since most armor beating moves aren't fast enough to beat Upball since it's so fast, and I'll bet most can't actually do like a d4 and beat both options, and command grab leads to a pretty effective okizume (TM) game for him.
Also, the choke. By far the biggest change for Commando and what now ties it together (Which it didn't before; without it, Commando made very little sense). NOW he has something that can make his strings and f4 safe as well as build meter AND set up a guessing game on block. -4 is almost perfect, since his parrys are either 4 or 2 frames, which would mean a character's reversal would likely be a 6-8 range startup or more. Add in EN command grab basically beating most everything but a jump or possibly a really low profile move, PLUS he has his own really fast two hitting EN move that is also safe (and no doubt would hit twice at that range), and Kano can actually make the opponent do SOMETHING after choke is blocked. This also means d3 xx choke and d3 xx command grab become different options because most will get out of ticks by jumping or going for an airborne move, which the choke will beat and now it can be safe for the effort (Armor still beats both, but when in Rome).
None of this probably adds up to super top, or even high mid, mind you, and it could probably use a little more tweaking here and there to be like super top, but it's a pretty decent variation now I think, and a dedicated specialist could probably do just fine with it. A lot of it is guesswork, and the damage isn't completely scary, but it's a variation that now makes sense. Those two buffs, small as they were, were probably more effective than you think, although getting the community to collectively get off its ass and stop feeling sorry for themselves is most certainly out of the question. And yes, I did move away from Kano to play Liu Kang, but I think I can spot a couple of good tools when I see them.