In my opinion, this show's characters are fleshed out, and this includes Bonnie. We had her connect (to a degree) with family in "Masquerade," and come to a pretty important conclusion about her witchy ways -- and not in a plot-point driven way, but in terms of her characterization. We saw her build a relationship with Jeremy, go through the ups and downs of teenage love, confide in him, care for him, fight with him and eventually get her heart broken by him. She's talked of her father, has the wonderful relationship with her grams, and recently we've seen background into her relationship (and lack thereof) with her mother.
We continue to get character motivation regarding her life and magic's place in it. Her fears about it, why she thinks she was given that power, when to use it and when not to, and choosing to do or not do depending on her humanity (both the good and bad sides of it). We've seen Bonnie fight for the greater good, fight for the life of her best friend, be there for both of her best friends, and be generally bad-ass in the ownership and use of her magic on more than a few occasions.
To say that she's "just" a witch does a true disservice to the actual character depth they have given Bonnie. Yes, she is the magic machine, but she's also a person with real, legitimate relationships with her grandmother, Jeremy, Elena, Caroline, Stefan (even if it's through Elena), Damon (even if it's antagonistic), Luka, Jonas (even if they're now dead) and Abby. One could just as easily say that Damon is just the token bad-boy/emo vampire, that Stefan is just the "good" vampire, but that does a disservice to both characters as well. There is more to them, and we are given witness to that. Do we see more of their relationships, motivations, etc? Absolutely. But they are the lead characters. Bonnie is a supporting character and yet we hear/know about her as much (if not more in some cases) than all of the other supporting characters.
The fact that I know her motivations, the reasons behind all of her actions in ways that have been both shown (by her actions) and told (by her words to Jeremy, Elena and Lucy) is proof of how fleshed out her character is. Over the course of two and a half seasons, we've seen Bonnie grow from disbelieving the witchy stuff, to being charmed by it, to seeing it's bad side, to using it in a bad way for a good reason (faking the despelling), to becoming wary, and too self-important over, to hating the situation it puts her in, to accepting and then embracing that she was given this power and can use it for good. And I understood her motivation of every step the entire time. That's pretty remarkable character development, and it's development I see with all of the characters (even some of the recurring). As long as I understand why these characters do what they do (right or wrong), get their motivation, see them react and act, do good, do bad, make mistakes, repeat mistakes, get better, grow and learn, I'm seeing some amazing character-work on my screen. And Bonnie is no exception in how I view the writing of the characters.
I honestly don't see Bonnie as a deus ex machina. We saw her relationship with her grandmother, and it was because of how strong that was shown that it had such power when she returned in "Ghost World." We see the ins and outs and ups and downs of her friendships with Elena and Caroline, with the ins and the ups always winning. We saw her fall for Jeremy, be in a real relationship with him, and get her heart broken by him. As for the witchy stuff, it just hasn't been 'oh, look she's a witch!' She's dealt with thinking it was cool, to being bothered by it, to wanting to having nothing to do with it, to using it too much, to basically ... constantly dealing with the ramifications and repercussions of being a witch. Outside of the main trio, we've seen more character work and motivation with Bonnie than any other. Just because her witchy powers ARE used a lot, doesn't mean that we aren't getting and haven't always gotten strong character stuff with her.
I know that some don't like the character and to each their own, but I don't see how she's ever been portrayed as just a witch when there's so much more that she's been shown as. I don't see how she's used anymore as just a tool than Elena is used as just bait, Damon, just the muscle, Klaus, just the bad guy, etc. All the characters can be given one-note descriptors, but I feel all of them are so much more, including Bonnie. As a fan of hers, she is so much more than just being used to further the stories of other characters, or as filler, as I have read suggested.
I've done a write-up of central characters for each episode of The Vampire Diaries, and Bonnie one of only five that I consider lead on the show (along with the main trio, and Caroline). And outside of the main trio, she's been the central character more than any other. ("History Repeating," "The House Guest," "Know Thy Enemy," "The Last Dance," "Ghost World," and "The Ties That Bind.") When gauging the central character per episode, aside from the trio, Bonnie is the only one who's had three episodes in a row feature her character arc, and she's beaten out Caroline with having more episodes highlighting her character, and has had more than anyone (again) except the trio. And even when she's not the central character, quite a few episodes feature her in scenes, moments, arcs that tell us what she is feeling, what her motivation is, and where she is at emotionally with those around her and her situation. I could pull out episodes, scenes, etc. going back to season 01 that highlight Bonnie, and it is a regular, recurring thing.
In "Ghost World," we got to see the strength of her relationship with his grandmother, her dealings with magic, her friendships with both Caroline and Elena (with both having her back), her love for Jeremy, and heartbreak over him, and finally her strength in dealing with his betrayal and showing some awesome self-respect. And in another episode, "The Reckoning," it wasn't even about her magic. We saw her choosing to follow Caroline's lead in finding the joy in life, being a great friend to Matt, and helping to save the day *not* using magic.
And when it comes to the friendships with Caroline and Elena, while we do see Bonnie there for the other two, offering support (and sometimes resentment as is realistic), we also see it the other way as well. Again, in "Ghost World," Caroline was ALL about Bonnie except for that final scene. Elena, even amidst the Stefan-drama, was on Bonnie's side with the Jeremy situation. "The Last Dance" and a bunch of Elena's discussions towards the end of season 02 were about saving Bonnie, keeping Bonnie safe.
I'm a big fan of Bonnie's, and I think she's awesomely portrayed as a kick-ass HBIC! She's a great friend, great girlfriend, smart, sweet, powerful and generally all-around awesome who is more reliable in getting stuff done than anyone else in the group aside from Damon. (Minus season 01, ep 20 through season 02, ep 04 -- even I wasn't that big of a fan of Bonnie as much during those six episodes.) However, overall, I think that Bonnie really is a great character with definite stuffies to admire, and I truly have never understood the contention that she's "just" the witch.