This game will have plotholes no matter what. People can find them in things before the ending. They can find them in things before ME 3 even. These writers weren't super careful when it came to such things, but for the most part, we all have a tolerance to it.
The ending exceeded the general audiences tolerance levels though. Whatever plotholes the indoctrination theory creates, they are minor and inconsequential compared to the plot holes it removes. The idea that the authors need to avoid "cliche" endings is a poor place to start from when designing one. The fact is that a good story's "original, unique" elements don't need to all come from the ending. When that becomes your goal rather than telling a good story, you become M. Night Shyamalan. In some stories it works, but it's bad to force it in if you didn't carefully plan for it from the start. It's really obvious they didn't plan for anything past the first ME when they released it. They're making it up as they go along. Would it have been nice to see the Reapers have a really deep, thoughtful, discussion-worthy motivation? Yeah. But it's probably not easy to make one up at the tail end of the game without stepping on the foot of something that came before. If an ending fix requires them to have some simple explanation that's not deep, that's fine. As long as it makes sense. There is a lot that makes the Mass Effect universe a well developed, interesting universe - one that took a lot of ideas together and gave them a good, unique flavor without an ending put a twist on it.
I almost wish "indoctrination" theory wasn't called a "theory" - it makes it sound like everyone suspects the developers planned it. We all know they didn't, or most of us do anyway. They did such a poor job writing, though, that they stumbled into too many plotholes to fix without a hallucination. Amazingly, they stumbled into something that's easy to explain based on what came before (the indoctrination video is impressive, anyone who denies it isn't giving the guy who edited it and uploaded it enough credit). Indoctrination is only a "bad" ending if it doesn't get additional material put on the end. Bioware oughto to adopt it and instead of calling what they plan to do a "clarification," just admit it's a change, a "fix" that actually fixes their worst problems and gives them a second chance to do it right. They need that second chance, and it will show a warped sense of writing standards if they show they don't believe that.
Of course, what we're all expecting is a clarification that doesn't adopt it. It's too bad though.Might as well "clarify it" by just having the Starchild break the fourth wall and tell the audience, "Yes, we didn't know what we're doing, we made this up at the last minutes, there is no further explanation, but at least now you won't speculate."