I would argue that the entire main plot of ME3 - chasing a MacGuffin and having a bitter twist ending where the Reaper motivation is revealed - is considerably weaker than the plots of ME1 and ME2. ME3 has amazing, gripping moments, like curing the genophage, giving the Quarians their homeworld etc, but the main plot itself is weaker than that of ME1 and ME2.
ME3 seems to somewhat negate the main plots and foreshadowing of the previous games, but it also demystifies the Reapers and makes them seem like simple tools, instead of the Lovecraftian, unknowable space monstrosities we were introduced to in ME1.
The human genetic diversity we are constantly reminded of during ME2 had an actual purpose with the original ME3 plot in mind, because humans were going to be used to stop the dark energy spread, so there was a point to the overarching Reaper interest in humans. But by the end of ME3, it turns out that Reapers just want to preserve advanced civilizations, to help them “ascend” - which would mean they aren’t particularly interested in humans. If it’s just the advanced civilizations they want, then why not Asari, Salarians, Turians, etc?
Harbinger comments throughout ME2 that the reason why other species are undesirable is that they aren’t genetically malleable and diverse enough, whilst humans have “impressive potential”. This tells me that humans were unique and could have served a higher purpose than traditional “ascension to Reaper form”.
We are led to believe that for millions of years,advanced civilizations at the pinnacle of evolution were harvested and turned into Reapers, not just the genetically diverse ones. It’s how Reapers reproduce. During the Prothean cycle, there was only one advanced civilization to deal with and Javik himself admits that one of the Protheans’ greatest flaws was that they lacked diversity and were too homogenized.
In my humble opinion, this was just a less than ideal way to end a trilogy.