I played these on a modded+banned 360 back in the day, so I was unable to get DLC or any patches (which also means no "extended" ending). I've now played through this like one and a third times (first all the games back-to-back, then starting from the suicide mission in ME2 to the end trying different paths in ME3 - and also because I made some terrible calls in the suicide mission first time around with predictable results). So, now I have seen all the DLC and the extended ending (two variations of it in fact). And I have to still agree with Mr. Horse:
I understand the challenges BioWare faced with the ending - having a meaningfully branching story in just a single game is hard, let alone if player choices must be tracked across three games. So I guess up to a point it was inevitable that it was going to be a "choose from these few options" kind of thing. And yes, how much you grind the games may alter the outcome of that choice, although how meaningfully can be debated. My problem is that once we learn what the Reapers are really about, the explanation seems quite convoluted and illogical. Sovereign said "There is a realm of existence so far beyond your own you cannot even imagine it. I am beyond your comprehension." - no, it is really quite easy to comprehend, it's just dumb.
I think the Leviathan DLC does do a much better job of explaining the reasoning behind the Reapers than the space kid (which is why I think it should have been a part of ME3 originally), but it still doesn't make the eventual choice that much more palatable. Also I'm a bit uncertain how the different endings would work in practice, especially the green one, but it's not like ME is 100% hard scifi so I'll let that pass.
But apart from whether the choice presented to you makes sense, one thing the ending lacked then and lacks now (even with some added footage) is that there really doesn't seem to be that much, if any, closure for Shepard and his companions. I'm not saying there needs to be a happy ending for all, or that there should be a lengthy epilogue, but by that point you will have spent easily 50+ hours with those characters and will probably really like at least some of them - it would be nice to know something about what happened to them (if they survive) in a world that's very different from the one you knew them in. No need for fancy cutscenes or anything, some simple "where they are now" cards would do.
As it is, for me the Citadel DLC (which was amazing) will henceforth be my official ending if/when I replay the trilogy later on. It isn't really an ending as such, but it's such a great distraction, you get to hang out with your buddies and have some hilarious conversations. So my headcanon from now on is that Shepard & co really fell off the wagon and just kept on partying - meanwhile the Reapers completed the cycle, but it was totally worth it, it was a hell of a party.