The reason why I dislike ME2 is because storywise you could cut it out completely without having series suffer a plothole. Only thing added by it is some attempt to develop Cerberus (very poorly because actions of Cerberus are inconsistent across the 3 games), Geth-Quarian conflict (which can be left purely for ME3) and EDI. Heck, you could make an excellent side-quest from ME2 for ME3. Just cut out every single new companion and their loyalty missions (with possible exception of Tali as hers is used to develop said Geth-Quarian conflict).
Starting right after battle for Citadel:
SR1 destroyed in Collector attack (Shepard survives)
Alliance rebuilds SR2 with new technology including a VI (that later becomes self aware, ie what EDI already did on Luna) and asks Shepard to investigate
-SR2 could have been in construction before destruction of SR1 to explain short amount of time needed
-Can also put finding the Crucible here, but at the basic stage where scientists just trying to figure what it is
Have Shepard visit 2 or 3 places (Freedom's Progress to learn of Collectors, Horizon to fail at stopping them and Derelict Reaper for codes)
Then go through relay blow up the base. Some gameplay changes during the base due to smaller number of companions.
Then have Reapers invade.
Drop the majority of Cerberus from ME3 (Mars, Citadel invasion and even Chronos Station) and you have game similar in length as current ME3. Thessia can be changed to work either without KL or have archives destroyed by Reaper right as Shepard is just getting to the building or something.
I suspect that I am biased, but I think the number of inconsistencies involving Cerberus in the trilogy is greatly detracting from the game.