@Matt Of course there will be another Metroid game, its one of Nintendo's cornerstone game series. I for one though hope this next game will take place after Metroid Fusion. As much as I enjoyed the 3 Prime games and the so-so Other M, I'm getting a little tried of all these "inter-equels" that take place between the older games. Its time to futher expand the story into the future rather than back into the past. And if they don't do that I at least hope they finally reveal who/what the hell was in that spaceship that was tailing Samus at the end of Metroid Prime 3: Corruption. That has been driving me crazy since as I saw it.
As for Eguchi, yea he did the Animal Crossing games but, he also worked on some of the Star Fox games, so maybe it might not be so bad?