Every game in this series has, at it's core, revolved around the idea of cooperation to achieve the unlikely or impossible. From an Alliance vessel filled with aliens chasing down Saren, to a Cerberus ship crowded with such a variety of races to go where none have returned, and finally a galaxy-wide tour, intent on collecting the support of all races and philosophies to stop an unstopable foe. This entire series is built on the ideal that differences can be overcome and the galaxy is stronger for that variety.
But the carpet is pulled out from your feet at the end. Even if the Catalyst's mission is righteous, it denies any achievements Shep has accomplished as ultimately worthless. The only solution to conflict is eradication, domination or eugenics.
You do make an excellent point. A consistent theme of the series has been victory through co-operation. The Suicide Mission. The plethora of aliens on the Normandy. The ability to bring an end to not one, but two sets of racial grudges (Krogan vs Turians and Geth vs Quarians), both held for centuries, and instead get them to work together for the greater good. Heck, the basic idea of the Council itself (ineffectual as they are, they still represent the ideal), and the ENTIRE plot of ME3.
Then the Catalyst comes along and says "Nope, this specific brand of co-operation is impossible, and I'm killing you all for it."
In a perfect version of ME3, the Catalyst would be represented as the ultimate challenge to the ideal. It would be the final opponent because it views the co-operation as impossible. And we'd beat it via co-operation, proving it wrong in the process. Or, alternatively, if the synthetic-organic co-operation was meant to be impossible, there'd better be some powerful evidence of that before the end. And then we can have an ending about finding an answer.
Instead, the Catalyst isn't framed as an opponent (despite being the Reaper leader) and we're expected to co-operate with it to help solve its problem of impossible co-operation. Oh, and the weapon that we use to win, the Crucible that was built and deployed via co-operation? We still need the Catalyst's permission to use it...
...Ugh.
(I might be a Control-headcanon-victory proponent, who can fanon my way around most plot-holes, but don't mistake me for someone who doesn't recognise ME3's problems.)
What good is bringing the galaxy together if the only way to save it is by the options it presents?
I cut the knot. I pick Control, consider myself to have proven the Catalyst wrong via Rannoch, remove the Reapers from the galaxy and leave the galaxy to heal. That's my path to victory. Though, yeah, it requires me, as the player, to just decide that Control doesn't go horribly wrong...
*****
You know, I realised recently that Rannoch is thematically inconsistent with the Catalyst regardless of which resolution you get.
Wipe out the Geth? You've proven synthetics can be beaten.
Wipe out the Quarians? Great, now you're working with the Geth, co-operation is possible.
Geth-Quarian peace? Co-operation is definitely possible.