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Mr. Casaubon is a late middle-aged, curmudgeonly, self-absorbed scholar. That's all that most people (readers and other characters) see in him. But that's just a trick of perspective, because we usually see things from Dorothea's point of view. Since we so rarely see things from his perspective, though, we have to do a little digging to get at Casaubon's character…
"But why always Dorothea?" (3.29.1), asks the narrator at one point in the novel. The fact that the narrator has to remind us that Mr. Casaubon deserves our attention, too, indicates just how much we're inclined to ignore him as a character. The narrator assures us that Dorothea isn't worthy of our attention because she's younger and more attractive than Casaubon – those qualities won't last. Besides, Casaubon's ugly moles and "blinking eyes" (3.29.1) are only on the surface of his character, and George Eliot likes to create the impression that her characters have active "mental lives" below the surface (see Dorothea's "Character Analysis" for more on that).
But Mr. Casaubon isn't the hero of this novel – far from it. He's not the antagonist, either. The narrator tells us that he's just living his life and dealing with his own insecurities like everyone else. He's not a monster or a villain, he's just kind of selfish. The narrator assures us early on that "Mr Casaubon, too, was the centre of his own world" (1.10.2). Of course he is – everyone is the center of his or her own little world. And that doesn't make Casaubon bad, just human. That's what the "too" means in that sentence – he's just like the rest of us.
The narrator wants to make sure we realize that Casaubon is just "like the rest of us": she stops in the middle of a sentence about Dorothea to ask, "But why always Dorothea?", and goes on to give us a lengthy description of Casaubon's inner life (3.29.1-5). She tells us that Casaubon has hopes and dreams that didn't work out, and that he is "spiritually a-hungered like the rest of us" (3.29.1). So he might be past his prime, and he might slurp his soup, and he might have unsightly moles on his face and spend too much time worrying about his research, but he still deserves our sympathy, because he's not that different from "the rest of us."
So if that's the case, "why always Dorothea?" If Casaubon is just a regular guy underneath it all, why isn't his point of view more important to the novel? Maybe it's precisely because he's just a regular guy. The narrator tells us that Mr. Casaubon's "soul was sensitive without being enthusiastic," and that his "proud narrow sensitiveness" wasn't enough for "sympathy" with other people (3.29.3). He's just a regular guy, sure, but that means that he doesn't have Dorothea's passions or sympathy. He's got a "mental life" going on underneath that mole-y exterior, but it's not as complicated as Dorothea's. His entire "mental life" can be summed up in a few pages at the beginning of Chapter 3, paragraph 29, while Dorothea's takes the entire novel. Casaubon is too stuck on himself and his own little worries and insecurities to be interested in the bigger picture. But again, this doesn't make him a bad person, it makes him average.
So the answer to "But why always Dorothea?" seems to be that Dorothea's able to see beyond herself to something bigger, while Mr. Casaubon is too absorbed in himself. Of course, Mr. Casaubon's self-absorption makes him miserable:
Instead of wondering at this result of misery in Mr. Casaubon, I think it quite ordinary. Will not a tiny speck very close to our vision blot out the glory of the world, and leave only a margin by which we see the blot? I know no speck so troublesome as self. (4.42.7)
The narrator assures us that Mr. Casaubon's self-centeredness is totally "ordinary," and that his "misery" is a natural result of it. The "self" that Mr. Casaubon can't get over is just a "blot" that is obscuring his vision. Sounds kind of pitiable, doesn't it? George Eliot wants us to thinks so: the narrator says, "For my part I feel very sorry for him" (3.29.3), and we (the reader) are supposed to feel sorry for him, too. But feeling sorry for someone doesn't necessarily make him likeable, and feeling pity for someone doesn't necessarily make him sympathetic.