I suspect he doesn't like them as well considering he often says he had very little to nothing to do with the Prime games (Which is true, I think he just pushes at the fact a little too hard sometimes) and tries to separate his work from Retro's with statements hes made in interviews. However, I've still never come across a source where he says the Primes never happened in the main Metroid timeline, so I don't know what he has to backpedal on.
As for Super and Fusion, at one point in Other M Samus explains that without the control of Mother Brain, the Space Pirates are a bunch of dumb, feral animals that can't function intelligently (Samus obviously words it differently, but that's pretty much what it comes down to). If this is true then how are the Space Pirates able to rebuild Mother Brain for Super Metroid after she's destroyed by Samus in Metroid 1/Zero Mission? If we consider what Other M says about the Space Pirates as canon then Mother Brain is never rebuilt and Super Metroid never happens which actually means that Other M can't happen either.
Fusion is screwed because of how the Power Suit functions in Other M. It's powered by Samus' mind (Emotions, willpower, something like that) and this is shown in at least 2 scenes; the Ridley scene and in Sector Zero when Adam ends up killing himself. In the Ridley scene, the Power Suit starts to remove itself once Ridley grabs hold of Samus and then completely disappears once Rildey drops her. In Sector Zero the suit starts to "flicker" on and off when Samus is stumbling after Adam before he enters Sector Zero and later dies. In both of these scenes Samus is totally out of focus and overcome with emotions which is why the Power Suit shuts down. This messes with Fusion because in the beginning of the game Samus loses consciousness when an X parasite enters her body which somehow leads to her suit needing to be surgically removed. Again, if we take what Other M says as canon then the Power Suit should have shut down and removed itself when Samus went unconscious which means her suit doesn't have to be surgically removed. Now if I'm remembering correctly, the X parasites got aboard the BSL station through Samus' infected suit pieces that were removed during the surgery and kept on the station, but if the surgery never takes place then the X parasites don't get on the BSL and Fusion never happens.
Admittedly, I'm not sure if I'm explaining the whole Fusion part right, but whatever, these contradictions were pointed out to me a while ago by other fans of the series.