I have a hard time understanding how someone can say ME1 is the best game out of the three.

I'll give it a shot.

Gameplay-wise, ME1 has many more RPG mechanics than its sequels and I wasn't a fan of their removal. They compromised a little in 3, but it's a toss up for me for which I truly prefer.

Really for me it's all down to the story. Chasing Saren gave you more of a solid villain to focus on, as opposed to the nebulous Collectors or the Reapers.

Once you discover the true threat on Virmire, Sovereign is a hell of a presence; intimidating and eldritch. In comparison, Harbinger (and the countless unnamed Reapers in 3) just don't seem to be nearly as imposing. Sovereign gave the impression that we are so far beneath them that we aren't so much as ants to them; they are so far beyond our understanding. Harbinger never really gave me the same impression. Even when he's only a mile or so away from you while you are running to get to the Citadel at the climax of 3, he's just... sort of there.

I also really liked the Geth as enemies. I feel like somewhere after writing ME1 Bioware really changed their minds on where they wanted to take them. ME1 has loads of references to how they have been evolving over the century behind the Perseus Veil and are becoming more and more similar to organic life, with their gecko-like Sapper units (which mysteriously never appear or even mentioned again). This one's just a personal disappointment I suppose.

Maybe the best thing about ME1 compared to the sequels is the same as in damn near every trilogy: the first entry feels like a full story. ME2 feels like it ends before the story does; you could probably play ME3 immediately after 1 and it wouldn't seem like much had been missed except some character introductions.