I stopped using official Retro Arch years ago, and I use SuperrSonic's RA version (also called HexaEco), but I can try and share some information. I have zero reasons to go back to official beyond the Picodrive core for Sega 32x support.
Each System has one, or several ways to be set to get a proper pixel ratio.
For example, while it is said that the NES has a resolution of 256x240, most NES games work at 240x224 pixels, and some of them at 256x224, with many side-scrolling games landing on the former. If you're using Retro-Arch at 480p, you should try setting the video at 480x448 (with both Horizontal and Vertical crop, option available in the Core Options, outside the Video Settings) or 512x448 (without Horizontal crop) for games that use the full horizontal image.
If you play them at 240p, then it would be 480x224 and 512x224.
SNES uses only 256x224, so it should be set as 512x448 for 480p or 512x224 on 240p, for example. Mega Drive also uses 256x224 for some games like Shining Force 2, while also 320x224 for others, like the Sonic games. so, 512x448 and 640x448 on 480p and... well, you get the idea.
PC-Engine is a bit different, it has two video modes like the NES or SMD, but they differ vertically. most of them are 256x224, but some of them are 256x232 if memory serves right, for some reason, and you have a handful of them, like Aoi Blink which have very weird resolutions, but they are just a handful...
A properly set Retro Arch, at least by my own experimentation, gives the sharpest, clearest picture you can get out of emulation on the Wii, but it requires either someone walking you through the settings, or... well, lots of trial and error like in my case. I actually have some Cores repeated with different video modes so I don't have to change the settings depending on the game.
Since I got an OSSC I've been using Retro Arch at 240p, so sharing my HexaEco config files wouldn't be too useful for most...