I know this thread is 3 and a half years old, but screw it, I'll use it as an excuse to share my thoughts on the two games. I played through P4 all the way for the first time very recently, got hooked, and am currently playing P3 FES that I bought on the PSN Store.
Story-wise, I'd say the two are on par when it comes to quality. Writing in both is pretty sharp for the most part, and it's keeping me interested. Two very different tones though, and I suspect that's the point at which people pick which one is their particular favourite. I think that Aigis is a bit dumb though.
However, in the turn-based gameplay itself, P4 is better. Persona 3's system of only controlling MC AND standing up taking up a turn makes for an occasional very frustrating experience. Have a Persona equipped that's weak to a certain spell that the enemy keeps spamming? Guess what, can't do anything about it. Furthermore, certain party members can be rendered useless for at least a good 5 turns this way. It can get incredibly frustrating. I'm all for difficulty, but punishing the player by keeping them trapped in an endless chain of attacks is too much. I suspect some of this might alleviated when I finally learn Me Patra.
The game also has issues when it comes to the Persona balancing itself. Because P3 was the first to introduce the concept of S. Links, the balance of MCs Personas all had to be changed to accommodate this and encourage the player to build the S. Links. Because of this, it takes quite a while for an individual Persona of the MC to level up, particularly in comparison to party members. This is to encourage fusion, which is where the S. Links come into play. Get an S. Link high enough, and you can unlock almost all the abilities of a Persona immediately post-fusion. On top of this, unlike his party members' Personas, MCs Personas run out of abilities to learn pretty quickly. HOWEVER, the game then has all these mechanics which seem to be dragging the player in the exact opposite direction, encouraging you instead to keep all Personas. Among these are the Fusion Skills (or whatever they are called), which require two Personas to perform. The first fusion skill you learn, Cadenza, is insanely powerful (50% HP regain and evasion up for all party members). However, to still be able to use this skill, you have to keep the two Personas that do it, and these guys fall behind in level very quickly. On top of that, you also have tons of weird ways to increase the stats of one particular Persona, as well as Personas that occasionally come with an item that only give it when you level them up enough. It makes for a game that isn't 100% sure if it wants the player to keep Personas or fuse them.
Anyway, the two points above you can attribute to P3 being a very different game then what was done previously, and to the credit of Atlus, both of the points were addressed and fixed for 4.
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