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It really depends on how mature the in-house tools are for a set game. For certain titles and genres, Nintendo have some specific needs that would probably be better suited to the custom tools that they've already developed in-house. The whole point of third-party engines is that a lot of functionality is in-place so you don't have to play around with it as much. If they already have that functionality in-house then there is no need use UE4 or Unity, in-fact they could be a hindrance if you have to make extra modifications for a specific game. For a new game/genre that's completely fresh, then a third-party engine could help speed up development.

Take Bioware as an example of a developer using a third-party (OK, not entirely third-party, but not developed in-house at Bioware) engine that's not appropriate to their needs. Their last few games have taken forever to develop and have been sub-par by their standards. A lot of that is because they used the Battlefield engine and had to do a load of custom work to make it suitable for their RPGs.