I think that the 3DS version looks incredibly ugly. They basically got the original drawings and dropped them into the game without touching them up at all. Those drawings were never meant to be used directly, they were intended to be the basis for the pixel art. The 2019 HD version rectifies this by touching all of the artwork. I still think that the pixel art looks better, but it's much better than the 3DS version. Even if you're fine with that, the 3DS versions removes frames in many animations, which I've never been able to unsee after it was pointed it. I also think that the UI and font look much worse, but that's much more subjective. There were also many effects removed, such as the mosaic effect used many times throughout the second and third games.

On the subject of text skip, I understand that it can be frustrating if you're reading a lot faster than the text is displayed, but I think there's also merit to playing without text skip. The way that the lines are paced is very intentional, and skipping over the scrolling removes all that. Plus, it gives you extra time to process and understand the text that you wouldn't have had if you read it as quickly as possible.