I can train everything 2-3 times a week too if I adjust my routine and I'm by no means someone who recovers fast... Recovery has nothing to do with it... Chances are you messed up somewhere with the lower frequency routine (diet, routine itself).
Anyway... Why do you only have three days? Can you at least go twice a day or something like that?
You can just add work to your full-body sessions, but after 6 or whatever big exercises, doing the other ones justice is going to be downright impossible...
Even if you were to do 2 full body and one "special" session instead, your weak bodyparts won't catch up if you train them less than the rest/don't make enough progress on the relevant exercises.
You could of course just focus on one weak area at a time, train it every session or something right at the beginning or whatever... But that's still half-assing it and it will affect the rest of your workout.
What is your exact routine like and how much protein do you eat per day? Are you gaining weight?
Only other way I see if you can really only train three days (...) etc, is that you realize that training is an equilibrium and something will have to give somewhere if you want to add more work to another area... Or in your case, include it in the first place... So, maybe instead of training your big movements 3 times a week, train them twice at most and spread that out over your three sessions, or maybe do it like this:
Day 1 - A
Day 2 - off
Day 3 - B
Day 4 - off
Day 5 - A
Day 6 - off
Day 7 - off
Day 8 - B
Day 9 - off
Day 10 - A
Day 11 - off
Day 12 - B
Those are just your big exercises okay? Half the body per session... Then train your weak areas every session on top of that or so.
If you can't gain strength on the ABABAB thing on your big movements, then you are doing something very wrong set/rep wise or so... That should not be an issue...