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Leynos said:

Giant Bomb is wrong. IS has never been owned by Nintendo. They are closely affiliated with Nintendo. They partner with hem. They feel like they are owned given how close they are but IS, is not owned by them. GB is a wiki edited by anyone and the only Wiki that lists that. Giant Bomb also thought Shulk was from Fire Emblem and Xenoblade was called Xenocross. Linking GB wiki is like linking Sega Retro.

Except from what I've seen they're owned IS used to be Nintendo R&D 1 I know that part is an objective fact to the point when all the R&D divisions were merged to become EAD R&D 1 remained and was merged into IS as subsidiaries have flexibility in how they're registered, for example Creatures Inc are classed as affiliates but are fully owned by Nintendo they are still registered as APE and appear as an asset on Nintendo's ownership under the registered name this is how Nintendo fully owns Pokemon as they own not only one third of the rights but also the private company that owns another third. The are various reasons for such practices whether for operations, business or tax.

IS to me looks to be a similar case where they're an internal development team like Creatures who are structured in a way to operate like a partner but in actually are still fully owned under their registered origin which is why they make development tools only for Nintendo, look at HAL for referenced who are an actual partner that weren't an internal team of even Gamefreak these two companies actually have work that are on non Nintendo platforms in their history IS however doesn't this points to Nintendo having full control. Likely IS are made to independently focus and create development tools like in their R&D1 days so the rest of the company is freed up.