Honestly...? Mass Effect's place there feels rather weak. You mentioned Battle of Naboo wasn't as satisfying ultimately because you don't take out the big bad ship. Yet even that is playable, Mass Effect 3's space battle however is a static event. It doesn't take into consideration any of your choices, it pays no heed to any of the allies you may or may not have. And no matter what, it always plays out the same way. On the other hand, the charge into the Omega Relay in ME2 feels a lot more personal. And if we are settling for cutscenes in this list too, I'd of much preferred that. Your choices, how you played, all the things leading up to that easily affects the outcome of that scene and the mission following.
As a player, Suicide Charge just felt much more epic than The Final Battle. Heck, while that isn't quite so much a space battle I'll admit, ME 1's battle for the Citadel feels more impactful as well, because your choices again are impactful. It's also the first time you take out a Reaper, and see that they can actually be beaten.