Games this flawed shouldn't be this good. It simply doesn't make sense. I've played games that had good ideas, but were dragged down by the flaws (Breakdown comes to mind), games that were decent, but could have been better, and games that are just plain bad. Mass Effect is infuriating at times, but still manages to challenge my beloved Ocarina of Time for the title of greatest game ever.
First, the flaws: The game suffers from really bad texture pop issues; a shame since the graphics are otherwise spectacular. The infamously slow elevators are a minor annoyance, but the random load times that often pop up are a bigger problem. The game's autosave feature is almost completely useless, only saving at important plot points and upon entering an entirely new area; On several occaisions my game session was cut short because I was too frustrated to play through a half-hour's worth of exploration because I didn't save. In combat, your allies are useless; when they aren't getting torn apart by enemy fire without putting up a fight, they're trying to use the same piece of cover you are, effectively preventing you from doing anything but running to a new spot. The Mako is fine for exploration, but as soon as enemies are added to the equation planetary exploration becomes an exercise in finding out what angle you need to be in relation to your opponent to actually hit them. Thresher Maws are even more frustrating, ultimately not worth the effort.
More importantly, there are two glaring problems with the RPG side of the game. There is a slightly disappointing lack of character development for the majority of your crew, with many interesting characters being forced into the background to make room for the love interests. some party members seem to only be in your crew to feed you information about their respective races. The biggest problem, however is the much-hyped dialogue system. You never truly know what you're character is going to say; all you get is a vague keyword or phrase that may not even have anything to do with what you end up saying. When compared to previous Bioware titles like KotOR, which gave you several well-written (often hilarious) dialogue options to choose from, Mass Effect's Russian Roulette method just leaves the player feeling cheated.
However, despite these flaws Mass Effect is somehow nothing short of brilliant. the story is excellently crafted: equal parts Star Wars, The Matrix, and Halo with a little Starship Troopers thrown in for flavor, Mass Effect somehow manages to feel completely new and original while paying homage to the Sci-Fi genre as a whole. Bioware also put an incredible amount of thought into the universe: one could spend hours in the codex reading entries on everything from Turian political structure to Alliance ship technology. What Lord of the Rings is to fantasy, Mass Efect is to Sci-Fi.
Bioware also finally succeeded in creating a morality system that doesn't force the player to be either a saint or a thug. the Paragon/Renegade system is simply the best thus far, allowing the player to follow the letter of the law, do whatever necessary to accomplish what they think is right, only care about themself, or any number of other distinct personalities. many choices will award both paragon and renegade points, allowing the middle-of-the-road morality that has been lacking in just about all games of this nature. Mass Effect also presents the player with genuinely difficult, game altering choices. Gone are the cut and dry choices between the easy way out with unpleasant consequences or the more difficult, "good" choice.
Mass Effect also takes all the tired, overdone conventions of the genre and turns them on their head. In this universe, mankind isn't the dominant species: they are newcomers that are looked on with fear and suspicion. More interestingly, the two most important Humans in the game, Ambassador Udina and Captain Anderson, are black. this is a major departure from the whiteout that pervades most of the sci-Fi genre, and fits perfectly with the theme of the game.
The game is also the beneficiary of a strange, unidentifiable quality that makes it endearing. It's impossible to describe. Maybe it's the feeling of a huge galaxy to explore. Maybe it's the frantic ending sequence, one of the more intense I've seen. Maybe it's the wide mix of emotions the game evokes. Maybe The game is actually a reaper in disguise, and I've been indoctrinated. Whatever it is, it allows the game to be more than just the sum of it's parts, and claim a spot amongst the greats.