There are already rumors about Metroid Prime 5. I think it makes sense because this time, Retro Studios can take on the project right from the beginning and already have everything in place: the engine, assets, the people they need to hire, project planning, mistakes to be avoided, and difficulties to overcome.
I think it's wrong to assume that Nintendo judges its IPs purely from an economical perspective; diversity in their portfolio is a very important factor. Even if an iteration fails, they don't just kill the whole IP. Metroid Prime is a prestige series to them. It is highly praised for its graphics, gameplay, atmosphere, and sound. It's their only series that truly speaks to core gamers who favor realistic and serious games (in a sci-fi sense).
Just because Metroid Prime 4 was a financial flop, it doesn't automatically mean that Nintendo will kill off the series. This time around, they will keep the costs in check (as mentioned in my first paragraph).







