Becoming god has always struck me as a very, very bad idea. Everything we have seen about the reapers has shown us that 'merging' with them results in really bad things happening. It's one reason why the entire ending was farcical - the reapers don't just efficiently mop up all higher life in the galaxy, they revel in doing it in an incredibly brutal and evil, genocidal manner. You don't merge with something like that and not expect consequences.
I don't really think I agree. The Reapers are brutal, sure but 'evil'? They are efficent in their work and brutality is more of a side effect, Sovereign and Harbinger looked at organics with disdain (which is understandable TBH) but they never seemed sadistic or overtly malicious to me, just machine-like cold.
I mean, the Catalyst itself says it in the end - the Reapers do not really seek war, they are a tool. They are doing what they were created to do "when fire burns, is it at war?" I understand this is unsconscionable from our point of view but can we really judge these billion years-old god-like machines using our own moral standards? I mean our own view of ethics is in constant flux and greatly varies from individual to individual, I don't
like the intelligence's solution but I see how it is logic from its point of view.
That said, the Catalyst was using the Reapers by following its original directive, Shepard's A.I. duplicate uses the Reapers following Shepard's morality. I don't think that there is something inherently 'evil' about the merge, they are tools and only as good as the one wielding them.
Plus, I don't think a god like elder race hanging around watching over everyone is a good result either. Much like Babylon 5, the entire purpose of the trilogy was to break the cycle so the younger races could progress on their own - not to have Shepherd God with an unbeatable fleet hanging around in case someone got naughty.
Clearly Babylon 5 heavily influence my view of the endings, but ultimately the only morally acceptable choice is destruction. Yes, it's ridiculous that Edi and the Geth die if you make that choice for arbitrary, 'screw the player' reasons but in my view it's the only moral choice. I was fully prepared to sacrifice earth and humanity to rid the galaxy of the reapers, and for both paragon and renegade shepherds the destruction choice is the only rational one for me. Compared to the literally millions of sentient species extinguished by the reapers, it's a small price to pay and it's the only outcome which removes them from the galaxy permanently.
It is true that Catalyst Shepard being around might stunt the Galaxy's progress but, again, it is still Shepard, if s/he thinks s/he's in the way s/he'll probably leave and watch from afar. I highly doubt s/he would become that unreasonable, then again, there's no way to know.
(I also have no issue with the destruction of the racial memories in the reaper, because they simply don't exist. Whatever process is used to create a reaper seems to totally destroy any aspect of that races being or beliefs. If all that's left are a bunch of memories archived inside the reaper, then it doesn't matter that they are gone because they weren't doing anything anyway).
Well, I understand why you would feel like that from an emotional perspective but I think that an archive on all of the living species in the Galaxy from time immemorial would have an immense scientific and anthropological value.