Here are the lore stuff that bugs me big time:
- According to ME1 lore, Vigil told us that when the Reapers poured through the Citadel relay, the shut down the whole relay network, crippling the Prothean empire, forcing them to fight from planet to planet, system to system (even Javik told this in ME3). That's why the extinction took quite some time for the Reapers, and that's why only a few (probably dozen) Prothean scientist survived in cryo. So why didn't the Reapers even tried to capture the Citadel and shut down the relay network? It doesn't make sense at all! Harbinger know Shepard, know what he's up to, yet letting him to use the relays?
- Mars archives: all of sudden Liara and TIM discovers the Cruicible plan on the archives. Humans studied the archives from the very beginning, that's led to the Charon dormant relay. And we only discover such thing now? It's out of place and according to my first point, Shepard's first route should be into the Citadel, using the data from Vigil and seal the station. That's the only way to protect it from the Reapers since they don't have a control over the Keepers (according to ME1 lore) so they cannot open it remotely. Also, according to ME2 lore, Vigil is not more functional so they won't be able to use the Ilos backdoor relay. Yes, this would make impossible to play on the Citadel, yet it would fit perfectly into the lore.
- The catalyst: As it is said, he's embodies the collective intelligence of all Reapers, and the Citadel is part of him. According to ME1 lore, the Keepers controlled by the Citadel. The Protheans used the conduit to go back to the Citadel and sabotaged the Keepers. So yes, they place a mass relay on the Citadel, "on" the catalyst, then sabotaged the Keepers, those Keepers who controlled by the Citadel thus by the Catalyst. Yet the Catalyst didn't sent a note to the other Reapers about the sabotage. Sovereign had to start an investigation to find out why didn't the Keepers respond to his signal, that finally led to Saren and we all know what happened with Saren.
- Pointless hintings and foreshadowing in ME2: It was hinted that the final coflict will be something involves dark energy and has to do something with human genetic diversity. None of this ever mentioned in ME2. In ME1 at the description of Dis planet about the Leviathans they wrote about a derelict genetically engineered space ship. In ME2 it is revealed that it's probably a Reapers since Reapers are do genetically engineered - that's how hintings work. Also in ME1 at the Klencory planet desricption it is stated that the beings of light are supposed to protect organics from machine devils and they have a crypt on the planet. This crypt part has removed in ME3 yet it would've been to place to find the blue prints of the Cruicible. Would've made more sense then the Mars archives....
- Meaningless Reapers in ME3: According to ME1 and ME2 the Reapers are some godlike sentient race of machines. In ME3 they're just tools without free will, who cannot even explain why are they doing what are they doing. In ME1 and ME2 both Sovereign and Harbinger had a big role. We even had en epic conversation with Sovereign. They were both masterminds, free of all weaknesess, independents, each a nation. In ME3 they're just tools even Harbinger himself. Also at the end of ME2 we saw at least 4-5 Reapers with different models and shapes suggesting that after each harvest the Reapers keep this cuttlefish style but yet they have a slightly unique look. Ofcourse not for all that would be pointless and impossible to make it in game. Howewer it does show a way how Reapers probably evolved over the billions of years. In ME3 we only see a slightly modified version of Sovereign and ALL the Reapers look like this (don't count those silly Destroyers and that possible "troop transport" Reaper hologram in the N7 mission). Even Harbinger's ME2 model were put in the bin and share the same model as the other Sovereign class Reapers, only he lacks the middle "leg" and has glowing eyes.