I'm wondering, how high are the development costs for the Prime series?
I mean, MP2 and MP3 (didn't play 1) both seemed to be relatively low-cost production (doesn't mean they're bad, far from it!)
The entire Retro Studios has around 50 employees (for a comparison, Bungie has ~ 150), which isn't a lot.
So I'd say the MP series are part of Nintendo's "hardcore" titles (like all of Intelligent System's games, but Paper Mario). They're relatively niche, and I don't believe Nintendo wants to do a lot to change that.
I have to say though, they aren't that low budget. I mean, compare these two.
Retro Studios: ~ 50 employees.
02/03: Metroid Prime
04/05: Metroid Prime 2
06: Metroid Prime Hunters
07/08: Metroid Prime 3
Intelligent Systems: ~ 100 employees
02: AW (1)
02: Fire Emblem (6)
03: Black Hole Rising
03/04: Fire Emblem (7)
04/05: Wario Ware: Twisted
04/05: Wario Ware: Touched
04/05: Fire Emblem: Sacred Stones
04: Paper Mario: tTYD
04/05: Fire Emblem: Path of Radiance
05: AW: Dual Strike
07: Super Paper Mario
07/08: Fire Emblem: Radiant Dawn
08: Fire Emblem: Shadow Dragon
08: AW: DoR
IS has released 5 times as many games (over twice as many pr employee) as Retro Studios, so RS uses a lot of time on each game (IS isn't a totally fair comparison though. NOBODY makes more games than them)