The bias that I bring to this conversation is that I think that motion aiming fuckin owns and has improved even the remakes it was haphazardly backported into (like Ocarina of Time 3D),let alone new games designed for it from the ground up.
At the time of Prime 3's release, the history of the Metroid series was marked by a staggering difference in popularity between America and Japan. I'm sure there was a sense within Retro Studios that they had carte blanche to pander to domestic sensibilities - especially given the prevailing attitude in the industry that players from different countries vastly different tastes. (ironically, Other M somehow contributed to closing the sales gap, and it has stayed closed subsequently, suggesting that it was only ever a matter of marketing, not of design.)
Anecdotes from the development of Prime 1 give some clues as to the difference in perception about the series. The language barrier contributed: one mechanic was pitched in which the player would be given bounties to hunt; the pitch was met with confusion by Nintendo, bringing to light that the use of the term "bounty hunter" in prior paratext had been a translation error all along.
In the genre context where they appear as protagonists (revisionist westerns and space jidaigeki), bounty hunters are, traditionally, antiheroes, and not made any less shady when the narrative affords them an opportunity to bring in a monster instead of a sympathetic fugitive. That colors the mentality brought to the characterization of Samus (who at any rate was enough of a cipher for conflicting interpretations to coexist). The traits emphasized were those compatible with antiheroism: she's feared, she's relentless, she's destructive, she's cunning, she's above all cool. So they put her in a power fantasy, where you pretty much just constantly clown on Space Pirates, who are effectively just in your way as you track down the cosmic horror that's your true objective.
The mainline series, by contrast, casts her in a more traditionally heroic light. She's cut off from her support, she's in the ruins of her childhood home, she's vulnerable, she's out there fighting for the cause of strategic arms nonproliferation (and if you want to talk about ideas that play differently in America and Japan, hoo boy). Most importantly, in Metroid games, she fights the final boss' minions, whereas in Metroid Prime games, she fights rivals who are pursuing the same target.
From a game design standpoint, I think a major element of Prime 3 that arises from Half-Life 2 influences or Halo envy is that in this one, Samus has allies. That's a new element for the series (the AI in Fusion is depicted as an obstacle rather than a helper). Ironically enough, taken objectively the Federation just in Prime 3 is a perfect mirror of the Space Pirates (competing for minerals with military applications, experimenting with Phazon-powered super-soldiers, employing formidable unique aliens with their own agendas such as Gandrayda and Samus, using a Mother Brain ), but I think that their overall positive framing is in service of that narrative design goal. The implicit amorality of the echoes* of the "bounty hunter" interpretation of the character well suits a story set in the backdrop of a war not between good guys and bad guys, but between our side and their side.
* pun intended