FES had better AI, then P4 had the best AI and manual control. Portable is straight up P4's core engine with some of the stuff from the original game, and a few changes. So it's kind of a mix of everything:
-Manual control (P4)
-awesome AI (P4)
-Getting up from being knocked down doesn't end your turn, but getting Dizzy while knocked down is a threat. (P4)
-Additional commands like helping someone up, follow-up attack (P4)
-Navigator tells you enemy weaknesses, not the weaknesses you've already found (P3)
-Three types of physical attacks (P3)
-The best cast of characters (P3 <3)
They change a few other core mechanics. Fusion spells are gone completely; now you get Spell cards ala more traditional SMT games. Getting tired also works differently; you can fight as long as you want, but it seems you won't get tired until you go home. To balance that out, returning to the entrance won't fully heal you anymore (it costs money). Combined spells from the first game are gone like in P4 (Cadenza, the best starting heal spell from Asparas+Orpheus, is now an ITEM, so you can't abuse it anymore). Personally I left the AI on for P4 and P3P because it adds to the role playing aspect of the games, and it makes battles more streamlined. It hasn't let me down yet.
Some other changes were implemented from FES to Portable, like the social links, and donating money at the shrine taking up time now (but now you can WORK at shops now, which ups 1-3 of your personal stats and gets you some cash). Managing equipment is done through the main menu instead of talking to people, and the weapons store doesn't frustrate anymore.
The tweaks definitely make it the best version of the game, even if the presentation took a hit, and the changes to both the original story and the female story give an added incentive to play again.
EDIT: Aw I liked the Endoscopy levels in Trauma Team. Just found it funny that you could turn around and NOT see the endoscope at all
My beef with the game was that Forensics took fucking forever!