That's a damn good question.
In one way it would be bestiality because they're technically "animals" but it seems they have a higher level on consciousness at least enough to understand human communication. We've seen the Pokemon throughout the series can understand what humans say and even respond.
This leads me to believe they're at least a step above regular animals in the realm of consciousness so therefore we can't really consider them animals but to be on the same level as humans might be a stretch.
Kind of a grey zone between bestiality and just downright degenerate.
I wouldn't be able to tell you if it's ethical or not. It may fall in the same category as children or dogs.