The basic premise is - what goes around, comes around.
ME isn't a grimdark setting. It's a fairly realistic one, which means that yes, being Paragon (the so-called high road) isn't easy, and he doesn't magically purify everything he comes in contact with. He uses a pretty rational and humane approach without being the Lawful Stupid (except rare occasions).
Remember that even with what some call a "fairy tale ending" - say, we destroy the Reapers, unite the races, et cetera, - it won't remove most of the basic problems. There will still be poverty. Earth will still be overpopulated. Omega will still be a sh*thole. The wide gap between the "big picture" with which we're concerned is illustrated by that mechanic from Horizon. Sure, he's a cliche, but serves his purpose.
In short, we won't be able to have a Star Trek-like near-utopia, but we'll do our job of saving the galaxy at large and making it a little better on average for everybody - that's the Paragon way. Doesn't mean Krogans will start crapping rainbows.