I'd have to disagree with your interpretation of Prime 1. What I felt is that (through the eyes of Samus) I had uncovered a lost chronicle of a super-advanced civilization slowly and tragically meeting their demise. The sense of isolation was on point considering that Tallon IV was probably, at one point, teeming with life, specifically the life of the Chozo. "Destroying" Metroid Prime felt rather cathartic in the sense that was the source of the corruption of Tallon IV's natural order. A lot of points in Prime made it feel like it was a mystery story. The tagline of the game purports as much, stating that "An evil force needs to be expunged from Tallon IV, but first...it must be found". Samus had missed the party (the party being the downfall of a civilization) and the player is given the opportunity to piece together exactly what the hell happened.
It was overall a very personal story for Samus, considering that the Chozo raised her, so I imagine uncovering the horrible truth about their fate was a tough pill to swallow.
I do agree that Prime 2 felt like the "filler " of the trilogy, but I take it as more of a story for Dark Samus.