why has this discussion gotten so personal so quickly?
Anyway, companion quests are usually fun, interesting, play with different settings and gameplay mechanics (it's often quite hard to fit in a shoot-out into a companion quest), involve lots of dialogue (which is a good thing, given that BW actually takes writing seriously), develop characters further, and generally play to BW's strengths - short, tight plots focussed on character development is something they can do. I think most people would agree with this?
What we're really debating is whether companion quests should act as side quests (as they do in ME1 or Dragon Age), or a mandatory feature of the main game, tied into the final mission's game mechanics, a la loyalty quests in ME2.
I think the mechanics of loyalty quests in ME2 is fairly contrived - I can understand that your crew will need to take care of some things, but that's something they should do on their own. It becomes very contrived when the crew members are new and don't know Shepard that well. Trust is something that's earned in steps, not made with one quest and some charm points, but taking the option to help out and have your friend's back on multiple occasions. For these reasons, I think actually the only ME2 loyalty quest that makes complete sense is Tali's - you have known her a while, if you helped her out in ME1 she's got even more reason to trust you with personal issues, and the public allegation of treason is never really "just personal stuff" anyway, it has political ramifications, serious enough that you probably have reason to deal with it now. The DLC quests also make a lot of sense - they're included as part of the bargain of Zaeed and Kasumi coming along in the first place (Zaeed's, in particular, only becomes a personal issue really by accident - it's a simple quest but well thought-out).
So I'd agree that optional companion quests which unlock based on approval levels, how far along you're in the game (and how much you've got to know them as a result), and dialogue options taken in the past make lots of sense. I also think ME3's system of adding companions to main quests relevant to them as kinda quasi-companion-quests works as a way of making dialogue as interesting and quests as involving as possible (I suppose it's hard to justify companion quests when the world ends - it's probably why there's a lot more cutscenes and non-quest dialogue).
As for failing/passing loyalty quests - if the circumstances fit, then sure, why not? It makes things interesting. It might be a better mechanic of turning someone properly hostile to you, or potentially losing them from your crew. As long as you can have a fair bit of well-written hostile dialogue where you can argue over your decisions (often, there's way more friendship dialogue than there is hostile), then sure. I'd generally caution against lose-lose scenarios though, unless you've taken some choices previously that put you in that position (e.g. in DA:O, if you kill all the mages in the mage tower, you can't peacefully deal with demon-possessed child later, meaning you lose a tonne of approval from one companion) - unless you've backed yourself into a corner by your own volition, often there's a logical way out.