Starting from the first game, the goal, as soon as you discover that Reapers are out there, is stopping and/or destroying them. I believe the bad guy of the first game, Saren, actually proposed something along the lines of synthesizing organics with the Reapers and surviving that way, and Shepard killed him for it and foiled his plan. And now we're to believe that the canon ending, or even one of the endings, is to throw away all you've been fighting for and synthesize with the things that you've been fighting?

That is inconsistent with the previous two games. Second, that means Shepard is making a decision for the entire galaxy, and every living thing in it. The Destroy ending also has him choosing to sacrifice the Geth and possibly EDI, so he is also making decisions he has no place making, but still the two incidents are on entirely different scales. It's likely comparable to razing and killing everyone in a town versus mutating everyone throughout the world. Third, why exactly is the thing talking to you and giving you these choices trustworthy? The Reapers are willing to just synthesize with organics? Where is the guarantee that the organics will have any free will left, or be anything more than puppets under Reaper control? Even that aside, what about the specifics of just what such a fusion means? Does every organic simply get nifty robot parts, or do they get an extra consciousness put into their heads, or what?

These are the issues as I see them. It is inconsistent, it comes out of nowhere, the information is unreliable at best, and at worst absolutely suspicious and a trap. Such an ending deserves no praise, imo, ignoring all the other issues that plagued the original endings, with their loose ends, lack of any closure, etc. The new dlc fixed those issues, but they're the minor ones, as you said, the things they added were obvious anyway, and we could all have imagined how things would turn out. The new endings don't change the fact that the endings are still as inconsistent and disappointing as they originally were.

That's my view, anyway. You liked the ending, and that's great. It's always better to enjoy something than to get riled up about it. But since you asked why people felt this way, I gave you my reasons.