Plus versions have added hardly anything that wasn't available for the vanilla versions via DLC (an extra playable character and a few new costumes here and there). The DX versions of the Arland and Dusk trilogies are essentially the Plus versions with the only new features being a run button and the option to increase the speed of battles.
The problem of vanilla versions is that the DLC prices are extremely greedy, so you are basically going into them with the knowledge that you won't have access to the extra dungeon, super materials and über-bosses. If you aren't a completionist, then the DLC is moot.
The recent influx of Plus and DX versions is owed to delayed releases for the Vita (Plus) and bringing games to Switch (DX). New Atelier games release simultaneously on Switch, PS4 and PC, so re-releases that are complete editions aren't going to happen anytime soon.