I have played through all three a few times and I still can't stand the endings. Yes they are a bit better with the extended ending dlc, but it still feels like you work so damn hard for hundreds of hours over 3 games only to be really let down at the end, no matter your choices.
**SPOILER**
Now that said with regards to the Geth and Quarians, I played heavy paragon throughout all 3 games and managed to get the two of them working together in the end. Basically the Geth have the reaper code and are more fully independant AI then ever before and are helping the Quarians reclaim their homeworld. And of course because of that the endings pissed me even more as the stupid little god child keeps telling me how AI and organics can never get along, yet I have proved that otherwise already. Frankly we should have had a choice to fight maybe use the crucibal as a weapon that say reduced or killed the reapers shields. I mean I spent so much time and effort uniting and entire galaxy like never before and managed to show on more than one occasion that it was possible to kill a reaper. See that is where your galactic readiness should have come into play. I mean depending on your choices it should have allowed you to win completely and save all the races, or lose most of them, or lose outright.
Now all that said and even with the ending the way it is, I still will say it is by far one of the best gaming experiences I have ever had. Playing through from 1 to 3 is such a blast and the characters are just great. Oh and that last DLC they put out, the Citadel one, was just great being able to hang out with everyone before the final push. Really showed the friendships (or more) that had occured over the games. Plus nothing beats Grunt being half passed out drunk in the shower.
edit: Oh forgot to add, I'm actually doing another run through again. Just have to do the DLC and final mission on the first one and then onto the second one.