Mass Effect - good but not great IMHO. Weak side quests that take place in barren landscapes, boring central character - Shepard typifies exactly what is wrong with most staid SF writing as he is a total bore - and rather average gameplay and interface. Not bad plot even if it is borrowing from many years of SF history and decent writing but nothing amazing. I'm hoping that Mass Effect 2 will be the game many make Mass Effect out to be. One note - I played it on PC so perhaps the weak interface was down to a poor translation from console, but either way if you release a game on PC I expect a decent interface that works well with a mouse.
Bioshock - good but again not great IMHO. Watered down version of System Shock that loses to much on the RPG side for average FPS mechanics and rather silly Big Daddy battles. Great art design and decent plot with one great twist and a few standout missions, but it was uneven in structure and went completely off the rails at the end. Again, I have high hopes Bioshock 2 will be the game many make Bioshock out to be.
God of War 1 & 2- very good but actually rather dull hack'n'slash mechanic. I love the story, character and narrative, but in the end the gameplay isn't that deep and the QTEs are rubbish - but then all QTEs pretty much are so far in games. But not the amazing God of gaming that majority claims IMHO.
Metal Gear Solid 4 (only one I've played) - decent story and gameplay but movement and interaction is weak for today, the plot is horribly overstated in delivery and the guy needs to hire a proper editor for every cutscene and listen to the guy (or gal). I enjoyed it, but with such archaic controls/actions it just isn't the amazing experience I expected from a gameplay perspective - I mean c'mon, Snake can climb onto one low cardboard box but not a shoulder high crate? I did love some of the set pieces and missions, but comparing its narrative to say Uncharted 2 it's clear that it's tied to an older set of ideas of character movement and interaction and level design. It does have decent stealth, but I think it lags Splinter Cell now in that regard. The boss fights are too over-extended too - particularly Vamp if I remember correctly, although to be fair I did experience probably the intended sense of satisfaction when I finally sank the syringe into the bugger.
Uncharted 2 - actually no, that's near perfect. Just kidding.
I was going to put in Halo 2 and Halo 3 (for SP campaign only, the MP is very, very good as advertisded) - but I really don't want to get into that arguementfest!
I noticed a lot of PC gamers have the same sentiment about the 2 games, and I can understand it. I would include those games in my too cracked up list, but at the same time, as you've stated, these are the first of their series, and there's bound to be mistakes. But what makes up for this is the fact that they have a lot of unexplored potential, like Assassin's Creed 1, and this was rectified with ACII. I've the same faith in their sequels.
As for the blue: I honestly feel if you started the series from the MSX2 PC days, like I did, and onwards, you'd truly be able to appreciate Metal Gear (or not, that would be for you to decide).
Yeah, I've noticed PC gamers like but aren't amazed by ME and Bioshock. MGS4 you may be right. The gameplay just felt a little off right from the start for me (although I appreciate the polish the game has, in that it is superb). I read the MGS databse prior to play (when stuff from MGS4 is locked out) so I didn't struggle with the plot, but I suspect if I was used to the controls from the start it wouldn't seem so odd. I just kept wishing why can't I move this guy like Sam in Splinter Cell?
I found AC2 to be a huge leap from the first, really good. And looking at released material I am pretty hopeful that ME2, Bioshock 2, etc. are really going to deliver fully on their excellent premise.