There are nearly as many different specific complaints about the conclusion of Mass Effect 3 as there are players who've completed the game. One of the major recurring points of contention, however, is the way in which the very final sequence of the game seems disconnected from the rest of play and from the series.
(Spoilers for the ending of Mass Effect 3 follow.)
Opponents of the ending argue, among other things, that the revelation of the Catalyst — the ghost in the machine of the Citadel, as it were — comes from out of nowhere, and that no previous hints have been left in the series to indicate that such a conclusion was even possible. A sharp-eyed Reddit user replaying the first Mass Effect game has found that maybe, there were hints all along.
As Commander Shepard explores the galaxy in Mass Effect and Mass Effect 2, s/he comes upon a great many individual planets. Most of these worlds sport thorough descriptions not only of their physical characteristics and mineral compositions, but also of their history or cultural relevance. The first game's codex entry for the otherwise unremarkable planet of Klencory (Newton system, Kepler Verge) describes a crackpot volus who might have been a bit of a prophet after all:
Klencory is famously claimed by the eccentric volus billionaire Kumun Shol. He claims that a vision of a higher being told him to seek on Klencory the "lost crypts of beings of light." These entities were supposedly created at the dawn of time to protect organic life from synthetic "machine devils."
Shol has been excavating on Klencory's toxic surface for two decades, at great expense. No government has valued the world enough to evict his small army of mercenaries.
Klencory can also be a destination for the Normandy in Mass Effect 3, at which point its entry has been updated to read:
Klencory is famously claimed by the eccentric volus billionaire Kumun Shol. His once-ridiculed visions of "beings of light" protecting organic life from synthetic "machine devils" don't seem quite so far-fetched now. His private army of mercenaries are well-established on the planet, waiting for husks to come knocking in on their door. In all likelihood, they will be obliterated by the molten metal of a Reaper orbital bombardment, on its way to somewhere important.
Whether it's a fortuitous coincidence or whether someone at BioWare was playing a very long game indeed remains a point of discussion. Rock, Paper, Shotgun points out that one fan questioned the connection many years ago but, like the volus Kumun Shol, went mainly unheeded. Until now.