When they were planning ME3. While we can blame ME2 for putting the plot on a treadmill for an entire game, ME3 still had conceptual problems of its own where the game went out of its way to shoot itself in the foot.
1. Having the Reaper fleet invade at the beginning of the game
Besides begging the question of why the Reapers don't just take the Citadel, this decision also forced ME3 to do what ME2 didn't and develop a way to defeat them while the Reapers are simultaneously rampaging through the galaxy. This also ties into the rather clumsy and poor handing of the Crucible as well. The game introduces it at the beginning and then plows into its war plot.
You could still fight Reaper agents without immediately resorting to a massive galactic war and the consequences that will have for the game. The arrival of the Reapers also deserved more build-up from a story perspective and more than a tutorial/intro level on the gameplay side.
2. Prioritizing resolving background conflicts in the setting while leaving the primary conflict with the Reapers underdeveloped
Something like Leviathan should have been in the base game not DLC. The Genophage and Geth conflict did not necessarily need to be resolved in this game and definitely should not have been if it is at the expense of what this game is supposed to be about (I also think the basis of the Rannoch arc really has problems with the context of this game but that is a topic for another thread). There is also the question if it is actually good writing to have one game resolve everything...
3. Dropping ME2's ball
While Shepard's resurrection and Cerberus get some deserved heat around here, these things would look much better if there had been some semblance of a Eureka! moment where the pieces snap into place in ME3. Instead Cerberus is indoctrinated and largely serves as an enemy auxiliary force and Shep's death is ignored outside of a few videologs on Cronos Station. The handling of Cerberus stands out as particularly grating as it squanders the characterization from ME2 and makes shoehorning them into that game look rather meaningless. ME3 didn't need something like a separate "Cerberus path" where the player worked with them instead but it did need for them to be used for more than they were. Mind control is very weak.
As an aside, revealing that they are indoctrinated at the beginning of the game doesn't seem like the best storytelling. Within the first 15 minutes the player is told that Cerberus are traitors, couldn't save that for a twist?
There are of course other problems like the poor transition between ME2 and ME3 that doesn't do a good job for veterans or newcomers but those could be largely patched up with better execution.