I found Commander Shepard almost indistinguishable from most other FPS protagonists in terms of character. I mean, yes, s/he is badass, but s/he feels a lot more like a blank space, like most FPS characters are supposed to feel like I could hardly be arsed to remember its first name. The thing is, the options and story become bland, and feel forced, I just want to say "Fuck this cutscene and its all-or-nothing options, let me blast aliens again!" To be fair, blasting aliens in M.E. is a bit more fun than it is in Half-Life 1, but I do indeed find Shepard boring, and could care less about him/her and the characters surrounding it. As far as space marines go, a lot more thought was put into it than the others, but, like Mario, Gordon exudes more personality than Shepard without saying a single word. That's saying a lot, since technically Gordon's face is only seen about 4 or 5 times throughout the game, and the most emotion he's ever expressed in-game was done with a crowbar.
Back on the subject of me saying "Fuck this cutscene" another thing I love about Half Life is that it expects you to find blasting aliens fun, it keeps the (in-cutscene) storyline focused on your goals and doesn't weigh you down with everything unless you genuinely give a fuck about the storyline and/or characters. That's the thing I love about the Batman Arkham series, one of the few things I like about Doom 4, It keeps the theatrics focused only on what's going on right now, lets you have all the fun in the world, and allows you to pick up on the story if it catches your interest. And the thing of it is, every time I've played a "storyline optional" game, (Even some somewhat insipid games like Daylight and the new Doom) I've been very interested in the story, and probably went through more trouble to get to it all then it did to have it spoon-fed to me by annoying cutscenes that I wanted fuck-all to do with anyway. Granted, this can be done right, there are a bajilllion games that can testify to that, but all in all, I just couldn't get into the story, and it was just me waiting for it to get over with so I could blast aliens again.
That being said, I never played any Mass Effect games from beginning to end, so I don't know if anything happened that could ever really change my tune, but I do know that the last one had a godawful ending that caused more rage than the last episode of the sopranos, and that Half Life 2 was able to hold my interest even when Mass Effect fell flat on its face.