Alright, my unnecessary input time. 
1st, i would like to say i haven't had much problem with Snake's AI. Its all about picking opportunities, like you have to do with Mr.X. Maybe if youre trying to suit a wider audience edit him and Jin's AI, but i honestly think they're okay.
And if not I can actually help with AI. Because i can code AI now, lol.
As for the vs. Mr. X matchup with Subby, its still very do able. Only took me three tries. If you are to change things though, as suggested by others, id say either make Subby's freeze actually freeze randomly, maybe 1/3 of the time, or have it freeze consistently and just code Mr.X's AI to anticipate it and crush the shit out of him with the leaping fist at random. Because then he's close, and you have to play to get a set-up, but its still fair.
Also, for those who would like Mr.X strategies from a fairly decent player:
Spoiler, click to toggle visibilty
Ken Vs. X
Move constantly, making sure to read the charging punches and leaps, when he is close, either go for the rolling throw(Ken has one of the most damaging grabs in the game) or if you have landed about two hits previously on Mr.X, go for your most reliable air combo for good damage, as the super armor breaks after about every third hit. Hadouken is a valuable "poke" when thrown out reasonably.
Subby Vs. X
Know coming in you are going to have to work your ass off to win this. Wait for X to charge or ground pound, then get close and use the command high punch(B+hp), pressing the command twice, as two punches will be thrown. X will catch you in this occasionally, but the quick recovery and push will make this reliable about 90% of the time from one or two steps away. After you should have an armor break, so go for a launcher if you have a safe opportunity. Abuse ice spikes at 1/2 screen away, and do the same with EX ice slide, its very safe as you pass through X, and may grant you an air combo if youre quick.
Jin S Vs. X
crouch HK, occasional grab, super cyclone when this bastard is close. Nuff said. Lvl. 3 is a great X fucker. Use blodia punch at distance if you feel lucky.
Timing is most iimportant, and you can get two grabs by jumping over X after one grab and going for one more right after wake up. Also can be used to sink the first grab.