Your latest answer especially by your last sentence. “What kind of relationship would make them happy.” What if they start to pursue your romantically or based on mating urge or such. Some may laugh but in a hypothetical pokemon world I think this would be a serious issue. I say it might be more common one might think.

The biggest issue for me here is that I just don’t believe there’s a whole lot we know for sure about Pokémon reproductive biology.  You can see what I have to say about that in this article here – and while I would be the first to admit that a lot of what I say in that piece is a little bit ‘out there,’ I think it does demonstrate fairly well that this is a tricky topic at the best of times (since the time of writing, we’ve also been slapped with the random NPC in Coumarine City who says that Pokémon eggs aren’t eggs at all, which is such a bizarre out-of-context statement that there’s little you can do with it, but could easily be Game Freak saying “yeah, whatever you think you know about this stuff is wrong”).  What this all boils down to is that I’m not sure whether Pokémon would be capable of desiring humans in that sense, or even whether they would necessarily have the requisite… er… bits… with which to act on it (even Humanshape species).

Having said that, let’s talk about this anyway for the sake of argument.  Inter-species breeding is certainly common among Pokémon, and in the real world humans often get different animals to breed and produce hybrid offspring like mules or ligers.  This kind of thing even happens without human instigation from time to time.  And then you have that… regrettable incident with the chimpanzee and the frog (a union which is not going to produce offspring no matter how you slice it)… Anyway.  I think the main reason we get upset when humans indulge in such activities (aside from the straightforward visceral revulsion – or, to put it in everyday terms, “eww!”) is that it’s just kind of an abusive action at its base level, because the animal probably doesn’t fully understand what’s going on and in many or most cases wouldn’t be able to do anything about it if it did – which on ethical grounds puts us in a similar position to sexual relations with children (again, eww).  If the Pokémon is the instigator, which I suppose could happen, then maybe there’s a mitigating factor there, but I don’t think you can get away from the fact that a trainer/Pokémon relationship is not entirely equal; I think most people in the Pokémon world would probably agree that the trainer is in a position of power or authority here.  A lot of Pokémon respect and look up to their trainers and habitually seek their approval; that’s really not a healthy starting point.  I believe the most appropriate real-world analogy would be a teacher/student relationship – sure, sometimes the student comes onto the teacher, but that doesn’t make it okay!  The proper response is to say no, firmly, and get the student transferred to another class (i.e. trade the Pokémon, because as well as you might work together, no good can come of that $#!t).  Alternatively, since a lot of Humanshape species are Psychic-types, people might easily suspect a reversal – I think that if such a relationship were ever publicly known, allegations of untoward Hypnosis or similar psychic manipulation would fly fast and thick, possibly ending with the institutionalisation of both trainer and Pokémon.

In sum: I actually don’t believe this would be common, and honestly I’m not certain it could happen at all, but if it did there are still serious ethical issues involved and the best course for the trainer is to avoid such entanglement at all costs because, really, letting something like that happen is not good for either partner, and although it might not have quite the same stigma as bestiality in the real world, I strongly doubt it would be received well (because, again, eww).