Will Nintendo owning Monolith Soft really affect the type of games Monolith Soft makes? If anything Monolith soft will start focusing more on RPG's. I'm sure Nintendo realises RPG's is one of it's weakest genres. Having a second party development team that is responsible for some truely excellent RPG's (some members of Monolith Soft worked on Chrono Cross when they were still with Square) working on some RPG's exclusive for the Wii (and DS) would be a great asset to Nintendo.
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Well, that's how I view it, at least.