Spoiler:
Gathering the army has a massive impact on what happens. The ending cinematic may not change, but what happens during the last mission DOES change depending on the choices you've made throughout the game, and most of those choices are going to be directly or indirectly affected by previous choices in the series.Also your stated plothole isn't really a hole. There are plenty of possibilities that make perfect sense as to why Sovereign was still left behind. Perhaps the AI was inactive during the events of the first game. Perhaps the Reapers aren't even aware that they are being controlled (much like indoctrinated people aren't aware that they're being controlled by the reapers). Perhaps the AI doesn't control the citadel itself, but only the reapers, and simply exists on the citadel. And of course there's the "dream" theory that GK mentioned earlier that seems to actually make a lot of sense when you break it down.
Simply because Bioware left some things open for discussion and interpretation doesn't mean the ending is inherently bad or doesn't make sense. It just means they wanted to provoke thought more than give a sense of complete and utter closure on the entire universe. Which makes sense seeing as there will absolutely be more games in the Mass Effect universe. And those games will likely answer whatever questions were raised at the end of this game