I know what dark energy is, but its theoretical existence is not the issue. Even if it was just something made up for the trilogy, it wouldn't make a difference. However, I find your definition of "major story element" rather suspect, since many things in the games can have their presence in the story be reduced by opting out of specific dialogue or skipping entire missions.
Well, you had a problem with dark energy as a story element (until now?).
Anyway, a minor story element is not critical to the plot. You know, only mentioned a few times and only used in a completely optional side-quest. A major story element, however, is plot critical.
The dark energy problem was clearly the Big Mystery element that was building in the story. A star experiencing billions of years of aging before its time is actually quite a big deal, and it was mentioned enough to be a memorable part of the game.
Dark energy was mentioned a few times in Mass Effect 2 and used in a side quest, but it wasn't critical to the plot and one could only speculate if it could ever become part of the overarching plot.
It doesn't matter though, dark energy theoretically exists, so it is absolutely fine that it was used as a story element in ME2. An overarching plot with dark energy engulfing the galaxy or something like that, was never used in Mass Effect. That's it really.
As for human genetic diversity, it's a big part of Maelon's experimentation, since he's using humans to formulate a cure for the genophage. However, major or not, the idea of humans being unique because of their genetic diversity is a terrible concept that should have died on the drawing board.
I thought it was only mentioned in ME3 when the genophage was cured. My bad.
It is certainly a pretty weak story element. Maybe it would have been better if they fleshed it out some more, or maybe not, I dunno. It is a good thing it was only mentioned in a completely optional side-quest though.
Then you have the other Big Mystery element dealing with the Collectors' sole interest in the human race, when, as Shepard points out, the reapers were trying to harvest everyone.
Frankly, the only reason why these things ceased to be major is because they were abandoned in the overarching plot. But, before ME3 came out, these things were actually important. Only now can people look at the trilogy as a whole and say this or that was just a small bit.
The Reapers harvest all the races when they reenter the galaxy, they don't build hybrid Reapers either. The Reapers wanted the Collectors to build a new Reaper with a human core, so the Collectors harvested humans to build a single human (non-hybrid) Reaper.
We could only speculate as to why the Reapers wanted to do this. I personally thought it was because Reapers considered humankind to be the apex race of galactic civilization (which is why they wanted to build a human Reaper) and also required a new Reaper Vanguard to do their bidding.
Anyway, the answer to those questions, and also as to why Reapers even harvest organics, was supposed to be revealed in ME3. Sadly, the writers just declared the suicide mission and an extremely large portion of ME2 as completely inconsequential. Like you mentioned, these story elements were actually important before ME3; like I have already written numerous times, the problem is that ME3 substantially disregards continuity. Bioware should have concluded the story in the direction as it was laid out in ME1 and ME2, i'm sure they could have come up with something very interesting and satisfying if they would have actually tried.