I would make the opponents dc to save go up higher and higher the longer the choke goes. Also if they break free they are staggered for 2 turns and can't talk if the grapple sustained for more than 2 turns. For the prerequisites I would make the bab requirement +4 considering grappling is a lot harder to pull off at higher levels. However I like your idea and I think you should go forward with it.
So I came across a topic about how the game doesn't support blood chokes, long story short I came up with this feat; what do you guys think? Does it seem balanced against the capabilities of other classes with it's level? Or is it a little overpowered? I really like the idea of a Rogue taking someone out quick and quiet, but suffocation via garrote is quite slow and really not a practical option. Also, a MMA style monk would be possible with this feat if that's your thing.
Blood Choke (Combat)
You have received specialized training to cut the blood flow off to your opponent's brain during a grapple, quickly rendering him unconscious (or worse).
Prerequisites: Base Attack Bonus +10, Improved Unarmed Strike, Improved Grapple, Choke option while grappling.
Benefit: If you exceed the target's CMD by 5 or more during your grapple check, you may attempt a Blood Choke in place of a standard Choke option. This functions as Suffocation, except the target treats his Constitution as 2 when determining the amount of rounds until he has to begin making Constitution checks. After 1 round of any round you do not maintain the Blood Choke, your opponent's blood flow will resume and restart when he has to begin making Constitution checks.
Normal: You cut off your target’s air supply so he has to hold his breath.
The "Choke Option" bit would need to be removed from prerequisites, and replaced by something like "Proficiency with the Garotte" since holding the weapon is the only way the option becomes available (as far as I can find on the PRD and OGC).
If your goal is to make it so that Rogues can choke someone to death, this is probably not going to help you in any real way. The prerequisites are too steep for it to be taken for most of the game, and by the time it is an option, it isn't worth three feats. I'm not sure that even if the Rogue somehow got all of the grapple feats available that it is a good/reliable option for them- it's going to be something like Strength Surge Barbarians that could make use of it with a consistent expectation of success (and consistent success is something you expect for several feats).
That said, I'm pretty happy that something like this is hard to do, since it's essentially creating a non-magical Save-Or-Die. Even if it's realistic, it's up there with "stealth neck-breaking" for things that I don't see how I can fairly incorporate in a game with any expectation of longevity. (I'd be glad to see a good representation of stuff like this that didn't become a double-edged sword for players, though!)
On the mechanics-
Do you have to constantly beat the CMD by 5, or simply manage it once, then maintain the grapple? I'm not sure after reading it twice.
It may bear a lot of similarities to Suffocation, but the way the rules are referenced is awkward. The duration you have given it is always set, so you don't need to play with Constitution in any way- this prevents people from accidentally transposing this "Virtual Con" into the Con checks later, or mentally giving things with no Con score a replacement one. Speaking of which, some guidelines for what can't be Blood Choked and when might be good to include- things with no circulatory system are fairly obvious, but what about people in fully-Fortified armor, or Alchemical Golems? People wearing a ring or magic item that don't need to breathe? I understand that the Suffocation rules are simply the mechanism you want to use to reach this end, but it might be better to take the bits you want to use and discard the rest, even the name, to get around the weird mental connections people might have.
Good luck on your designing! Some other things for inspiration or short-term problem solving: Strangler feat (Ultimate Combat, for Rogue choke problem), Tetori Monk (for MMA Monk shenanigans)