It's a daunting and challenging--but intriguing--idea. I recommend reading Tim Lebbon's Fallen if you haven't already. It's quite a good read that primarily uses two alternating VP.
The main characters are two very close friends that have a bitter, bitter falling out in the first few chapters and find themselves divided. They end up racing to reach the end of the known world.
In all fairness I think one character's POV is a little more sympathetic but they both screwed each other over badly. But neither of them is exactly the kind of person you want to stand up and root for. I'm not sure if that's sort of what you're going after, or if you'd prefer two perspectives that the reader **will** stand up and cheer for.
Either way I think it'd be worth your while to check it out to see what Lebbon did with the two main characters' VPs and see if it inspires any ideas for your own project. Good look!
I'm new to the writing craft, but am also an avid reader. Hopefully you get something out of this.
The movie The Prestige. Excellent film. If you haven't seen it, see it. If you have, skip to next paragraph. Basically, it's about two contesting magicians, played by Hugh Jackman and Christian Bale. An accident at the beginning causes Jackman's character to lose his wife in a trick performance. Bale's character had proposed the possibility of tying a different sort of knot for her to escape from in the trick. At the funeral, Jackman asked "Which knot did you tie?" Bale responds. "I don't know." That response sends the two apart and begins a contest of sorts, first they sabotage each others' acts (Jackman throwing the first punch out of grief), and then it becomes a goal to out-think the other magician for each of them. The ending is quite interesting...
Despite his flaws, I continuous found myself favoring Jackman's character. Likely cause? Reader's sympathy was well established at the beginning with the loss of his wife. Maybe I also just preferred his performance.
The beginning of the story favors Jackman's point of view as well. You never doubt that the story is about both, but you see a little more from Jackman's eyes. This stacks up with previous posters' advice that I saw.
Alternatively, you could go the direction The Dark Knight did. The Joker was a completely despicable character in terms of moral make-up, but it also made him fascinating, and easily my favorite character in the movie. One way to go might be to make one of your characters someone who the readers are drawn to in spite of rather than because of themselves, and have the other be palatable and entertaining. Unlikely given your plot description, but possible.
Inevitably, readers will pick sides. One way you can keep the balance a little is to keep them guessing, like Rowling did with Snape. I love Snape as a character, and am glad he turned out good. But I also would have loved it had he been the Machiavellan villain I’d heard one theory call him, topping even Voldy and being the real antagonist. If you change the circumstances surrounding your characters, it’ll keep them wondering who’s going to do what.
Hope you get something good out of this, and good chance to you!
On the other hand, I would point to Polanski's Ghost Writer as an example of a taut and lean and tightly resolved thriller very much dong Seventies-era avoiding of "feelgood" compromises that came out this year.
Saw that. Had a bit of trouble /not/ thinking "OMG, McEwen gets sum Jane Fairfax, the lucky git"