I've heard that Latvala was chosen over Mikkelsen because Latvala has more experience from developing cars. Also the reason why Hänninen is driving this season is that he's the main guy developing and testing the car and it's a part of the development program to complete the season, not to collect maximum manufacturer points.
I didn't know Meeke was negotiating with Toyota, but after Rally Finland 2016, I think anyone would have wanted him.