Wow I had no idea I was running it at 4:3 I was so excited at how crisp and smooth it played that I didn't realize. Plus I haven't played this game in over a decade anyway.
Anyhoo I downloaded the pnach file because that other link seemed incredibly complicated so I used the pnach file and it looks MUCH better.
I think this is how it's supposed to look right?
I used to think why is everyone so short in Persona 4 lol.
You've got the aspect ratio great now! Now just from personal opinion, there's are probably some tweaks I would do.
It looks like even though you're using PNG's, the files look compressed. Are you sure the website you're using isn't compressing the files? I like to use Minus to make sure my pictures show up online exactly as I took them with no compression.
Assuming your computer can handle it, I would make sure that the emulator is rendering the game at the same resolution as your monitor. What I'm thinking is compression might just be that your rendering the game under 1080p but taking screenshots at that resolution, which would make everything look a little messy. If you are rendering at your native resolution, and you think your computer can handle it, try using some Anti-aliasing! It'll make the game look much smoother and more natural.
Lastly, the colors seem a little off. Especially in "Command" on the bar on the left. Perhaps mess around with the settings in SweetFx that you're using and tone them down a bit?
Those are just some things I thought while checking out the shot, I hope it helps.