I would be surprised to hear of any game that is as moddable as Skyrim, let alone a JRPG.
I don't know about the "feeling of a fantasy isekai anime" but there are a few open world anime games that released in the last few years. Random list, because I haven't played them:
- Tales of series (Tales of Arise, its most recent entry, garnered a very good reception)
- Sword Art Online, the anime that started the isekai craze, has a few video game adaptations. AFAIK they are not great games, but fans of the original material seem to enjoy them.
- Dragon Quest series (the latest title, DQXI, was unanimously praised).
- If you dig the futuristic/pseudo-futuristic aesthetic, games like Star Ocean, Xenoblade/Xenoblade Chronicles, Edge of Eternity may be up your alley. They are all open world anime games.
I could try more aimed recommendations if you went in more detail about what kind of specific "feeling" are you looking for. Comfy/chill adventure in some generic fantasy land? Character-driven story? Being overpowered from LV1?