Unfortunately, it matters far less to any company why a product sold poorly than the fact that it sold poorly (not sure I'm explaining that well). In this instance, Nintendo is not making games out of the goodness of its heart. It's making games to take our money. That's not just Nintendo; that's every company in every industry.
Whether Federation Force sells poorly because it's a hack Metroid game or because Metroid generally sells poorly comparatively to Nintendo's real big sellers like Mario and Zelda is immaterial to Nintendo. Metroid isn't a system seller, and Nintendo has tried a few times to make it one. Gretchen, stop trying to make Metroid happen. It's not going to happen. Metroid performs modestly. The best selling game in the series is the original Metroid Prime, and that didn't even break three million. The reality, unfortunately, is that sub-three million units is not good enough to justify millions in development and a couple of Nintendo's best teams in Retro Studios and what is now what, Nintendo Entertainment Planning and Development (it's complicated what happened to Research and Development 1 with all the mergers and reassignments).
I understand why Nintendo would change Metroid in this way. Its trying to figure out a way to elevate the series. The problem is that Nintendo is asking the wrong questions and complicating a really simple truth. Outside of the series' own relatively small yet dedicated fanbase, it just doesn't resonate with most people. This is coming from someone who is on record several times that Metroid is his favorite series. While Nintendo keeps asking itself what it can change about the series to make it more palatable (e.g. add voice acting, make it more action-y, make Samus less mysterious, change the art style etc.), it ignores the fact that changing Metroid makes it not Metroid. As much as I enjoy 3D Metroid, I honestly think the best solution is to go backward. Give it to a small team with a small budget and make a straight 2D sequel that speaks directly to fans because it knows exactly what it is. That game isn't a system seller; it's a game that turns a profit zeroing in on a very specific audience.
Nintendo doesn't want to spend a Zelda-like budget for not Zelda-like sales. That doesn't mean Nintendo will never try again or Retro Studios will never go back to Metroid. It just isn't priority for them. The counterargument I always hear is that Nintendo is destroying goodwill. These are the same people who complained day after day then still bought a Wii U (eventually). You're part of the fucking problem then. That's why I make a concerted effort not to continually whine about things I don't like. Metroid Prime: Federation Force is not my cup of tea so I move on. If I wanted to vote with my wallet, I'd stop buying all Nintendo things. There's no use lying to myself; I'm not going to do that. However, I can save myself $40, and just accept the fact that Metroid Prime: Federation Force neither speaks to me as a Metroid fan nor a consumer of video game things. Still, I sincerely hope others find it enjoyable even if I can't and/or don't.