persona 3 story bosses are a joke, and the tartarus bosses often go down with the same strategies: use status changes to have assisting enemies help you or use a persona with a magical defense to what the enemies are using while you attack their weakness (when possible) and keep whoever is useful alive. fusions are more important than actual battle strategy, and can be very frustrating due to the random skill inheritance.
also, i'm talking gameplay IN GENERAL, not fighting mechanics. persona 3's gameplay consists of fighting and social links. tota allows you to explore the world and has actual sidequests. persona 3 also has a terrible dungeon design and no puzzles, whereas tota is the opposite. p3 has a very limited world too, it's like 20 screens total.
persona 3 has horrible character development, with the exception of junpei and aegis. the other characters are depressed for 1-2 weeks, keep bringing up that same theme for this meantime, then their personas go ssj. in tota, the characters have their issues throughout the whole game, but it isn't constantly hammered to you. there are also multiple conflicts.
anyway, the themes themselves are cliché for both games (war, cloning/dangerous science, redemption, friendship, treason, whatever). still, tota has a character cross a point of no return without blaming someone else (like cloud giving sephiroth the black materia because of mind control) and it doesn't happen before the game begins with the character being evil or something dumb like that. there is nothing particularly mature in persona 3 to make it stand out as some new jrpg standard tho, which is what your posts seem to imply.
