Hmm, recent times I'll say Bethesda due to the fact they haven't currently brought out their Action adventure sequel to an RPG (Despite me not liking Oblivion at all) and I guess Fallout 3 came out after it which many older school fans disagreed with but it was solid
Bioware... Well Bioware are just brilliant, seriously bringing out Gears of War with a story as their sequel to a brilliantly made RPG was gutsy and despite my hatred for the move (Not the game, just the leap away from RPGness) they succeeded... than they made DA2 removing any praise I just gave them
Square... same as Bioware for me for many years... than FF13 came out...
If it's pure history I'd say a tie between Bioware and Square, modern times I'd say Bethesda because they've disappointed me slightly less lately (Probably change if Skyrim disappoints)
No Atlus? :/ Doesn't Persona count as an RPG? (or JRPG. but it's still an RPG.)
I'm a little cautious in voting for Bioware because though they make wonderful stories they are starting to slack a bit in terms of gameplay (and environments but I'll let that slide.)
In the confines of your 3 choices I'd say Bethesda. The only Square games I really love are the first Kingdom Hearts and the original Final Fantasy. Bioware and I have a bad history so I steer clear of their games entirely. As for Bethesda, Morrowind makes up for all bad they've done. I've got 8 years of that game under my belt and I still love it. I can recite the entire opening cutscene to the game. Even now I'm still finding side quests I never did!
Out of the 3 choices I'd pick Atlus. It all started with Contact, 2 weeks of my life gone in that game. Since then I've learned to love Persona.
Bethesda games are poorly made from the RPG standpoint, but are complemented well by their free choice and free world mechanics.
Bioware games are generally really well designed, but have this huge problem in that you feel complete with the game 2/3rds of the way through. also, ever since it was aquired by EA their games have been seing a steady decline as the respective IP's are milked for every dollar they are worth; For every Dragon Age and Mass Effect which are absolutely great from the RPG standpoint, you have a Mass effect 2 and Dragon Age 2 which absolutely destroy the RPG mechanics for 'better flow'
Square Enix is really the only choice considering they not only have some of the Best RPG titles i've seen, but also that they continually push the bar with their development. And while some of their progress has been in the wrong way and lead to horrible game (cough*Final Fantasy XIII*cough) it is still some sort of progress.
I've never really enjoyed a Square Enix RPG, but I liked ME1 and 2 and Dragon Age and Fallout 3 and Oblivion. I vote Bioware because although I think Fallout 3 is a bit more fun than Mass Effect, Bioware's characters and plots have always immersed me more in the story.
That's not a very good comparison. That's essentially asking if we like structured, story-based RPGs; J-RPGs, or open-world, sandbox RPGs. The three make very different types of games, and it's not really possible to say which is better.
Going just on which games I like best, I'll go with Bethesda. I love my open world titles.
Black Isle made the best RPGs ever. Baldur's gate, Planescape Torment, Baldur's Gate II, Icewind Dale. And BioWare worked with them back in the heyday of RPGs, so my vote goes with them. They've also made Mass Effect, Dragon Age was awesome because it was basically Baldur's gate again in 3D.
I vote Obsidian because because those are people who still make true RPGs despite the bug ridden games that get fixed a bit later.But haters gonna hate.Since they are in Bethesda right now I'm inclined to vote Bethesda as they have titles I enjoy in there.