Poker Academy's NL has an advisor, lets you stack the deck, freeze the button, and replay the hand, TTH NL does not.
On the other hand, the PA advisor doesn't explain its reasoning at all, the TTH Limit advisor sort of does.

My gut feeling is that TTH is written by old fart poker players who are also old fart computer programmers, PA is by
AI whippersnappers who picked up poker or picked the brains of poker experts.

I have both. Trying to second guess the advice differences in similar situations is an interesting exercise.

PA runs on under Mac OS X, a big plus for this disgruntled ex-Intel employee.

Actually the key thing with any simulator is to play each hand very methodically instead of lapsing into Quake or Doom rapid-shooter mode. And analyze situations yourself using your reference collection instead of blindly following the advisors.