From what I read, Sakamoto doesn't consider the Prime games canon to the Metroid timeline.
At some point they must consider it at least as a second or alternative timeline.
Now, about Other M. I don't like what they did with Samus as a character. I mean, in the game like this with so many cut scenes, such a huge emphasis on story and all that it's not okay not to give her voice... it's just downright stupid and... unfortunately they overdid it. Gameplay wise the game was really good imho and i like what they did with the combat, amazing animations and all that, but the first person view was not okay at all, especialy if you compare it to Prime series - night and day. Visuals and art was also realy good along with level design with some minor issues.
Overall, i just and simply enjoyed playing this game and it was the first 2.5D Metroid game done right in terms of gameplay alone. I get why so many people don't like it but it was not a disaster or anything like that in my eyes, it was a good game if you simply forget about story and Samus stuff which so many people just do not wan't to do. Sure it was a linear game for the most part but so was Fusion and Zero Mission for that matter and i don't see a problem here as long as it's fun and interesting to play gameplay wise.
Also, i don't understand why they've outsourced 3DS game to MercurySteam after so many people didn't liked and hated what Team Ninja did with Other M. I mean, it's a different developer and all that but yet again it's not their in-house team. It's not like i don't think that MercurySteam can't make a really good Metroid game... it's just i don't like what they did with Castlevania game which was extremely linear and not very interesting in terms of gameplay and level design - all of this was extremely basic in comparison to Symphony of the Night and especialy map and level design. But the videos i've seen so far was really good so i have high hopes for this game and REALLY hope they won't fuck up the map and level design this time.