Kirby's in a pinball game.
The Pokémon are in two pinball games.
Mario's in a pinball game.
Looks like they felt it was time for someone else, especially someone like Samus, who can actually turn into a ball, unlike Mario (WTF), to get into a pinball machine. Sure, the world of Super Mario may be all happy and colourful and cheery and magical where something like this is more acceptable, but is it really blasphemy for Samus to try this out?
Sure, when I first read the header, I was like, what's the deal with this? "Metroid pinball? How wrong!" I'm a Metroid fan myself. But I think the problem is that so many fans of Nintendo are sort of niche-fans, not quite cult fans but they're not exactly the largest group out there any more. And, as I've seen with things like the Neo-Geo, the more of a niche you are a fan of, the more you treasure it as it is. Fans of Metroid have always thought of the games as following a continuity, so the first time Samus gets a spin-off game it's an outrage, apparently. I remember people spazzing about Metroid going into 3D before Prime actually came out.
I'm sure the first impression of this game is going to be "WTF", but I'm guessing not many people are actually going to be fretting over it until the game comes out. And if it's a good game, what's the problem? Simply accept it as not part of the continuity, a little quirk, but if it's fun, then enjoy playing it.
I mean, look at Super Smash Bros. Melee. Some crossovers make sense. Several ones, especially the big ones, don't make sense. Apparently no one seems to mind the fact that Samus is trading blows with Pikachu, but her being a ball like she already does in several Morph Ball puzzles is somehow weird.