Admittedly I've only played two of Monolith's games, Disaster Day of Crisis and Xenoblade. The latter was utterly incredible and one of the best games of last gen, but the former was a real mixed bag.

Retro, on the other hand, have produced three great games, (Prime 3, DKCR, DK:TF) one good one, (Prime 2) and one of the best of all time. (Prime)

I'd say I like Monolith better. Not only was Xenoblade absolutely amazing, but I also really like Baten Kaitos, Xenosaga, and Attack of the Saiyans.

Though, Intelligent Systems is better then both of them.

Did love the Metroid Prime games from Retro (haven't really liked sidescrolling platformers since the N64) and Xenoblade and Baten Kaitos from Monolith, I would have to say Monolith.

If Xenoblade Chronicles X is as superb as its predecessor, and Retro's next game does turn out to be Diddy Kong Racing 2, I may very well change sides and hold up Monolith as Nintendo's new flagship studio.