This is ridiculous.
Nintendo and Square split because of their own differences. In fact, the real reason was a disagreement over the N64's use of the cartridge format. They packed up, and moved over to Sony's CD-format PlayStation. Quite simply, it was Nintendo's own folly, and as you probably don't know, from the time of the split, up until just before Final Fantasy Tactics Advance was released, both companies were very bitter towards one another. In fact, before they split, Square was considered one of the closest development branches to Nintendo, hence Super Mario RPG. However, aside from offering Squaresoft an alternative, Sony was relatively uninvolved, contrary to what you seem to think.
As for other series, like Conker, that's because Rare left Nintendo, and was bought by Microsoft.
You have your anger in the wrong places.