If a Final Fantasy appeared on the GBA and has some patches (audio, font, decensoring, possibly other things) then that would tend to be my pick over SNES and whatever vintage Japanese console* it otherwise appeared on. Certainly over the PS1 (though they serve as not unreasonable options if that is what you have), DS as well (though I might take up the mantle of 3 there) and certainly whatever nonsense they did for the recent PC retreads, android and IOS fed the PC stuff sometimes so eh but definitely not definitive.
At the same time the NES/SNES stuff was the main target for many hackers over the years and that makes a compelling counterpoint when the volume of stuff available, as well as recreation (assuming it did not otherwise happen ahead of time) of whatever perks the later stuff got.
*I am prepared to have someone discuss the various video qualities of things here to find it is the technical best like we might for say Resident Evil 4 and its dozen ports. That nobody seems to be doing much with them though tells me most things I care about.
Dragon Quest I have not really played enough of to say here, certainly not played for comparison.
Don't think we really have any megadrive vs SNES in the RPG comparison stakes. Bomberman, platformers (Aladdin being the more notable), fighting games, racing games, sports games, things that were still better on the Amiga... all good for comparisons but RPG wise I think it was pretty much exclusives right down the line. Both have some great ones though.
Similarly if something started life on the Amiga then it should probably be experienced on that if your alternatives as the megadrive/SNES.
PCE/TG16 vs elsewhere is probably going to be left for bomberman and castlevania fans to fight over, maybe shmups as well but I know less of that and is way off topic.
I could maybe see an argument for some of the older might and magic games on the consoles vs PC and other things. Would almost be personal preference/personal history with the games though and it would be a hard argument at times.
What became of Wizardry I will have to leave for another day, mainly because I don't know enough about the later efforts.
Megadrive vs Saturn in the Phantasy Star world though... tricky, even more so if you are not a Japanese speaker as most have not yet been properly translated. The ages games are very good though.
Don't think Dreamcast saw any ports of things from older devices on the RPG front (barring THUG Pro it has the best versions of older Tony Hawk games a lot of the time) but I might pick the Xbox version of Shenmue 2 over its one. Gamecube version of Skies of Arcadia will probably be the definitive version there as well but there is not an awful lot in it, and both are hideously expensive (saw a GC version in a shop the other month for north of £100) for what they are -- it was a good RPG at the time and definite step into the future of such things but I would not pay that for it today saving that I flip it.
I would very strongly urge reconsidering playing the Phantasy Star 1 and 2 games on the GBA form, though if it is what you have then do it. You are going to want a megadrive for 4 though so why not go there from the start. I generally suggest avoiding 3 so no worries there.
I would probably say the same about any GBA ports of things in general as well, though with patches many of those are enough to say you did. Breath of Fire could be an exception though. I believe we don't mention Lunar Legend in polite conversation.
I would probably pick the remake of Megaman Battle Network 5 for the DS over the GBA versions at this point (and indeed as most are so similar if you want an intro to the series then that, even over 6 on the GBA). Only time I do that for DS RPGs that appeared on the GBA as well. If you insist on playing the GBA Riviera over the PSP version (I would not suggest the game at all) then could be justified. Never liked Chrono Trigger but the amount of hacking work the originals have means I am unlikely to suggest the DS version, even if the flames would keep me warm for years to come and apparently some consider it a definitive version (not sure when that one happened).
Are we counting PS1 as classic for these purposes? Because I am not sure what I would do about Final Fantasy 7 through 9 there now with various vintages and versions of PC ports that were the base for a lot of very good hacking work (and drama), never mind the recent remake (which I have not played -- was waiting for it all to be out first). Hoshigami: Ruining Blue Earth Remix I would take on the DS over the PS1 version I think.
Fortunately I think that is the main debate here as not a lot of PS1 goodness has ever appeared in non basic emulator format elsewhere really just yet. Though I did see Grandia got a treatment a couple of years back (Switch and then PC) so might have to look into that one, and I never played the Saturn version that the PS1 got ported a few years later.
Final Fantasy Tactics: The War of the Lions, nominally being a PSP (and I think IOS) somewhat enhanced remake/update of PS1 Final Fantasy tactics (for many the best of the Tactics series) probably wants to be noted in this. Tactics Ogre saw SNES, PS1 and Saturn versions, as well as a PSP revisit and GBA sequel (only one of those I have any time in). However I am not sure tactics games particularly count in this.
If I am debating the PS1 then xbox does not really count there, and for non exclusives that is mostly Elder Scrolls Morrowind, Fable, Bethesda stuff and Arx Fatalis for which you would be crazy to not go for PC and mods there. Will mention Deus Ex 2 just to get the hairs to raise up on the back of someone's neck.
Baldur's Gate Dark Alliance and its sequel might see the xbox as my device of choice though, though that is more dungeon crawler and there are some mods on PC that make it compelling (and "definitive" usually means money no object as it were so I guess I have a nice LAN setup in that case).
Not sure what goes for N64 vs PS1 vs PC in this timeframe as far as RPGs - I can talk about Turok and Forsaken but that is not RPG. It was also the last time it really made a lot of difference in terms of PC vs console, give or take the occasional bad port (see Risen on the 360 vs the PC) or oddities like James Bond Nightfire where the PC effort was basically a whole other game.
Could do N64 vs later things. I would pick basically every other version of the Zeldas (I count the Zeldas as an RPG, much to the seeming annoyance of some) over the original, but that might be more because I consider the N64 basically unplayable today. Whether I want to count the 3ds ports over the gamecube efforts I don't know. Equally as soon as the decompilation efforts for the N64 Zeldas reach some level of maturity (never mind 1:1 compilation) then all bets are off there like Super Mario 64 is today.
Xbox 360 vs PS3 might be classics in some circles now, prices certainly seem to be heading that way and we are now technically two generations on, but I am not counting that. Not to mention I already compared things there a while back elsewhere (turns out PS3 = RPG machine is nowhere near as strong a claim there as it was for the PS2 and PS1 give or take Ni No Kuni and a late stage showing from NIS) and frankly most things there appeared on PC which is going to be the best option these days -- might have been bad ports then but increasing computing power and modder efforts mean the distinction is kind of pointless right now. That said Eternal Sonata (a very nice game, I have the 360 version and it is one of the things that brought me back to Japanese RPGs after burning out big time) and Nier fans that speak Japanese might have a word or two with me here on the PS3's behalf. Have not played the PS4 version of Resonance of Fate at this point either.https://emulation.fandom.com/wiki/List_of_notable_SNES_ports_and_remakes
has some more though I will note a lot of the GBA stuff has patches.
Enough waffle for now.