Developing a Prime's worth of content takes time.
If there is a Metroid Prime for home consoles in development, it will target the next Nintendo console.
Metroid Prime series produced Kensuke Tanabe spoke to Eurogamer at E3, and confirmed that the time to develop the amount of content in a Metroid Prime game would take several years.
"It's a long time but it would need to include a lot of content, which would take a lot of work on the development side." - Kensuke Tanabe
The interview also indicates that the game would follow new plot threads after a couple of the long-standing ones were cleared up in Metroid Prime 3: Corruption.