The other thing that gets my goat is that I suspect in the minds of some players , and I might hazard a guess, some of the writers, that Thane didn't have enough of a connection to the main plot line. Problem is, he's at the whim (mercy) of the writers for that! I love pretty much all the characters in ME, but consider this for a moment: Garrus, not exactly needed to move the plot along. His involvement in ME1 was really just about how he wants to "get" Saren. That's really it. Ashley is just "found" alive on Eden Prime.....they lost Jenkins, and she is Alliance, so "come on, girl!" Kaidan.....he's already on the ship; that's pretty much it.
I think you can see where I am going with this. Many of the other characters aren't any more important to the main storyline than Thane. Garrus has been there since the beginning; so he's got longevity going for him.....I guess.
BUT, here is my main point; I personally LIKED the idea of the majority of the squaddies (former and present), having their OWN story lines, and how they relate to Shepard. This being <slight sarcasm> an RPG, that is how I hope for my NPC interactions to be........added sub-plot, flavor, romance, introducing new lore, comedy, ect.......... As for ME, I always saw the relationships as giving Shepard a real reason to fight. The more Shepard cares and interacts with his squaddies/crew, the more motivation she/he has to save the Galaxy. Save his friends/family (squad/crew), and the Galaxy reaps the benefits.