Yeah ME1 kinda sucks, especially in retrospect. The story had always bothered me a bit even before ME3 but I let it slide. Post-ME3 though I find it hard to ignore the glaring flaws in both ME1 and ME2.
One of the things that bugged me about ME1's story was the beginning actually. It was never very clear to me why a Spectre was needed for what was essentially just a pickup mission, or how Nihilus could gauge anything of import about Shepard from such a mundane task. Was there some threat they were aware of or anticipating prior to the mission that the game never bothered to inform us about? They were caught off-guard by the Geth attack so they had no kind of prior knowledge about that. It just seemed a bit vague and clumsy to me.
Another thing that bothered me was the bit of a plot hole regarding the accusations against Saren. The identities of Spectres are supposed to be classified, yet a lowly dockworker identified Saren by name, even though Saren claimed not to be on Eden Prime to begin with. How could a dockworker possibly know about Saren then if Spectre identities are kept secret? Isn't it kinda obvious that Saren is lying? Doesn't anyone on the Council or otherwise think it's kinda suspicious that a dockworker was able to implicate someone whose identity is supposed to be classified on a planet he was not supposed to be on? Is the Council really that inept or did the writers just not quite think that through?
And one more thing that bugged me was the explanation (or lack thereof) for the purpose of the Reapers' "harvest." What is it about their goals that are incomprehensible (barring the extremely convoluted explanation in ME3) exactly? It is implied there is a purpose but the only real "explanations" given is that the purpose is unfathomable or that it doesn't matter. It felt like a cheap copout used to cover for a writer who didn't know or really care about what he was doing and just made **** up on the fly (which ended up being exactly the case).
Those are just some things about the story that bothered me. There are of course the recycled environments, clunky inventory, tedious planet exploration, repetitive combat, etc. that work against the game but those are pretty obvious.
All in all ME1 was a messy start. Its saving graces were the companions (aka Garrus and Wrex - the rest are kinda annoying really) and some sharp dialogue. ME2 was an improvement in most departments but it was not without flaws either. And don't even get me started on ME3... 