True, the Rachnid Queen ending episode did have that weighty feeling of being an important decision that you didn't want to to screw up. That's half of what a great RPG should include. The missing half was any consequence in the rest of the game. Sure, there might be something in the sequel, and that would be interesting. But it's just a throwaway gimmick in the main game because you never see any result of that decision. They couldn't even bother to write in a brief news message for the elevator ride about a fresh Rachnid attack, or the Queen being observed fleeing to uncharted space.

(IMO) the Rachnid Queen episode was just "RPG Lite" salad dressing like the final Wrex sequence, or decisions about which party members are sacrificed. All heavy-seeming decisions on the front end, with no effect on the game world. Shepard could basically do no wrong, and make no bad decisions, even if he/she wanted to.