I don't think the problem is that the ending isn't happy. I've seen plenty of fiction that does a downer ending very well. Dark Knight, Empire Strikes Back, Revenge of the Sith and the Incredible Hulk are ones that come to me right off the top of my head, and generally they're pretty well recieved (SW prequel criticism aside).
The problem is that there is little to no reward to the ending. This is especially important for a video game where consumer investment is required, and exponentially more so for a game where choice and consequence is touted as the central feature. We need to get something out of all the time and thought we put in, an emotional payoff for our becoming involved in the story. There's no clear path from our choices to the conclusion we get. Rather, the conclusion just happens arbitrarily. BW could have even made the ending work if they'd just tweaked it to reward us a little more for playing their product. Show our war assets winning or losing the battle. Have heroes and villains we've encountered and influenced either kick some serious ass or go down in a blaze of glory. And then, when we finally get to the Catalyst, we can face one of two attitudes from the kid.
1) We've pushed the Reapers back, it actually looks like we're winning. We may have a shot at earning our own peace. The conversation with the SC is a little more guarded. He's cornered, and we may be about to destroy him. He tries to bargain, explains his purpose now that his back's against the wall, and pleads with Shepard to help him resolve the conflict he was designed to end. We have a choice- help the Reapers fulfil their purpose, or refuse to use their technology and gamble on winning with the assets we gathered. The colour chart choices or a successful refuse are all possible.
2) Positions are reversed. We're the ones losing. SC sees that this is happening, but decides the cycle will never end unless it changes. Its tone in the conversation is more that of someone doing a favour for someone else. Its talking down to us. It has chosen to give us this chance to end the conflict. Cue colour chart or our total failure.
This would give you a potential pool of eight or so endings- the RBG endings, with the flavour of us pushing the Catalyst to offer them or of the Catalyst pitying us and condescending to help end the cycle, giving each a completely different flavour. that's six alone. Seven- total annihilation. Eight- Victory, if you have enough for the first scenario. After that, you can have variations on whether shepard survives, the Normandy survives, the squad, etc. Its really not so much more than they made already, but that little extra makes it all the more palatable and makes the ending entirely of our making, not the brat. It properly rewards us for going through the narrative.
As it stands, it feels as though the writers used the ending to reward themselves with some haughty philosophical message rather than properly rewarding their consumers.