that's kind of a hard thing to nail down isn't it? are you looking for more of a sandbox game, god game or something else? I guess the 'lots of customization' is throwing me because that's the root of a lot of RPGs to begin with.
Maybe you can help me narrow it down

are you looking for
1) Lots of Equipment Slots
2) Lots of Stats
3) No set Path
4) Lots of Side Quests
5) No Clear Goals and Objectives
6) User Generated Content
7) Other?
I can't say why... but the first Saga Frontier for PSX is coming to mind, as is Star Ocean for PSX. Both of these games are quite vast but in different ways.
How about Unlimited Adventures for DOSBox... that game has an insane community and number of mods that popped up around it.
Dungeon Hack on DOSBox... very customizable for how challenging or easy you want the game to be with tons of replay ability through randomly generated dungeons.
Shiren the Wanderer on SNES (with English Translation) is one of my go to games. It's a rogue like that is one of the best in my mind. It's tough as nails to get started, but as you learn the game (more about personal progress than character progress) it really opens up. There is also a vast amount of extra content/challenges to work through. Yeah the equipment choices are limited, but the way the inventory system is handled it really is a very pure rogue like.
Minecraft through Android? I mean my goodness there's tons of customization there.
I still haven't tried Fallout in DOSBox/QEMU yet, but somebody must have, and that games is pretty customizable and wide open to explore.
Have you found anything yet that meets your criteria?
