I had no issues with flying and swimming in the Banjo games.
I'm wondering if we should have Laylee-driven flight in Yooka-Laylee though. Flight is a bit of a level breaking ability; they solved this in Banjo by using flight pads, but I always wondered why Kazooie couldn't just fly whenever she wanted to. On top of this, Laylee looks too small to carry Yooka...
If flight isn't an ability that can be used all the time, why have it at all? Perhaps we should just have a flying transformation instead, a bit like the bee from the Banjo games.