I just watched the commentary on the miniseries DVD, so I can relay some of the creators’ rationale on certain points.
They’re not making him overtly evil on purpose. Really, he is kind of a schmuck. He was a self-promoting, self-absorbed media figure back on Caprica, more famous for his reputation than for his accomplishments. Six, the blonde Cylon babe, played him effortlessly. She appealed to his vanity and to his egotistic incuriosity about women, and trapped him into helping the Cylons destroy his entire people. He never wanted that. But now he’s complicit, and he is choosing to remain complicit rather than confess his terrible role, out of a combination of extreme guilt and shame plus a certain urge toward the power the Cylons clearly represent and are sharing with him. That makes him a villain: But he’s a human villain, weak, self-centered, short-sighted, instead of a larger-than-life supervillain of some kind.
This impulse toward the human informs all the characters. The least flawed guy on the show so far is Gaeta, and maybe we just don’t know him very well yet. 
Seriously, in the commentary, the creators talk about how the actors are inclined away from shallow heroism and toward exploring their characters’ flaws. For example, they talk about being impressed that Jamie Bamber, the guy who plays Apollo, is willing to present the ostensible hero with an unlikable edge. And he is, certainly: erratic, touchy, occasionally irrational, not well grounded: not the way this type of character is typically portrayed, and risky for the actor if viewers are alienated and misplace their dislike of the character on the performer, but very worthwhile if the balance is right and you pay it off later.
But this creates an ambiguity in the drama. You can never trust that the heroes are doing the right thing, or are correct in their perceptions and assessments. You cannot release yourself to live through the heroes and become vicariously heroic yourself; you have to maintain a certain amount of distance so you can evaluate the character’s moral choices, even while you’re being drawn into their humanity. It’s harder work than watching escapism like Trek.
And note that Trek and SF like it is presented in a high style, with a theatrical tone that emphasizes the fantasy. It’s safe to be carried away by that kind of storytelling. That’s not the case with highly naturalistic material like Galactica, where you have to take a more active role as a viewer, thinking about what’s going on, considering the moral quandaries, asking yourself what you’d do.
(This stylistic choice is connected to the physical design choice, by the way. Another reason for the stylized acting is to sell the fussy faux-future design they’re surrounded by. In the commentary, the creators joke about the audience pointing and looking at “the sci-fi chair!” It would be disharmonic, obviously, if the actors were standing in front of the weird furniture and sparkly walls and not acknowledging the strangeness somehow. So, conversely, because in this series they wanted a naturalistic acting style, they had to combine it with a naturalistic world so it wouldn’t look odd.)
Final word on the acting style: You’re right to compare it to The West Wing. That’s exactly what they’re doing: a human drama that happens to take place in this other world with this other technology. That’s what science fiction does best, reflect our humanity back to us, rather than our love of gadgets.
Which brings me to my final point: These “please help me not hate something” discussions rarely help the requester to do so, I think. No knock on you as the OP, because often, it’s simply a matter of taste. And taste, of course, is entirely subjective. Just because other people like something doesn’t mean you’re obligated to like it. For comparison, I’m almost entirely alone in my circle of acquaintainces for finding Will and Grace basically unwatchable. People are surprised to learn that I feel that way, and they ask me if I’ve seen such-and-such an episode because “that one was really good,” and, y’know, it isn’t that. It’s just, I don’t like it. I don’t like the tone, I don’t like the jokes, I don’t like the stories. It just doesn’t appeal to me. And I don’t let it bother me, because I reject the notion that I’m “supposed” to like it.
Maybe that’s happening for you. Maybe the combination of the low-key style (see, for example, the scene in the miniseries where Adama gets the call with the first news of the Cylon attack; Gaeta quietly reads a note, Adama acknowledges it, and hangs up: no melodrama at all), the real-world physical design, and the morose, mourning emotional tone just isn’t to your taste. Maybe it’s something else. Maybe something rubs you the wrong way for vague reasons at the moment, but if you were to come back to it in five years you’d suddenly see something different about it. Or maybe not; maybe it’ll never appeal to you.
Nothing wrong with that, y’know.
Maybe it would be worthwhile for you to get a hold of the DVD, watch the miniseries, then watch it again with the commentary. Hearing the creators explain why they did what they did, and what they were going for, may help you. Or maybe you won’t buy into it, and the stuff that bugs you will still bug you. Me, I wouldn’t stress too much about it.
