My take on Federation Force is Nintendo is working on Prime 4, more then likely what Retro is doing but it's still years away from release. Since it's been 5 years since the last Metroid game and Prime 4 could still be years away, Nintendo might have felt a spinoff like this would be a nice way to show the fans they're still committed to the Metroid franchise by giving them a different take on the series.
Problem is, they need to announce the real deal before showing a spinoff like this. If Hyrule Warriors had been revealed with no talk at all about a new real Zelda game, fans would have been furious. Had Prime 4 been revealed at E3 as well, this game would be viewed a lot better then since Metroid fans would know the game they actually want is coming and more open to getting a different experience on the side.
Of course I wonder if the negative reaction might force Nintendo to come out and actually say they're working on Prime 4. Kind of like how at the end of E3 2008 with all the negative covered from their conference that year, Miyamoto actually said they were working on a new Pikmin game.
Miyamoto revealed Pikmin on the last day of E3 that year so there's still time for Prime 4.