This is a good post. Also, in a previous thread it was added that Lincoln had the backing of Yamauchi's son-in-law in all his decisions, which was probably a powerful force within Nintendo. I wonder if it's true that the shift towards Japan was indeed a company-wide decision.
I could maybe see it making sense given the situation at the time: Nintendo had lost almost all their ground to Sony when it came to Japanese third party support, so they probably felt the need to put a lot of resources towards rebuilding those bridges, which they did start to during the GCN era. Also, back then few people could really predict how important western developers would become in the console space. Sure you had games like KOTOR and Morrowind exposing American console gamers to uniquely American-made games, but nobody could have predicted that Microsoft would jumpstart the next console gen before Japanese developers were ready for it, opening a void for western studios to fill. And even then, could a more aggressive NoA really have out-negotiated Microsoft for the cooperation of the western developers coming from the PC? Could more games from Rare, Factor 5, NST, Left Field, and Silicon Knights really have competed against the likes of Bungie, BioWare, Bethesda, and eventually Epic?