Maybe you should include an "other" option? I mean, there's more protags than just these four...
Anyway, for me, Jill>Leon>Chris>Claire.
I noticed this because I tend to not like Chris Redfield very much. Every time he shows up, I know I'm about to get an action heavy resident evil title, and those tend to be my least favorite. But even in RE 1, his most horror focused title, I found Jill's playthrough much more interesting.
Chris is kind of in a weird place for the series, at least in regards to RE1.
On one hand, I'd argue that Jill in RE1 (note that I'm referring to the remake) has the better story, in as much that I find Barry's plight more interesting than anything with Rebecca. On the other, Chris's path is arguably the 'true' story, in that this is meant to be the catalyst of his vendetta against Wesker (and vice versa). It's also much harder than Jill's, and you could argue that makes it 'truer' as well - Chris has to survive on his own, Jill keeps getting help from Barry.
Chris is arguably the closest the series has to a main protagonist, but going by the poll, he seems to be the least liked of the "big four."
This led me to wonder if I had a bias against him, or just the titles he was in.
Well, thing is, by my reckoning, Leon has been in more 'action titles' proportionally than Chris.
Confining this to core entries and excluding remakes, we have:
-Chris: RE1, CV, Revelations, 5, 6, 7 (4 horror, 2 action)
-Leon: RE2, 4, 6 (1 horror, 2 action)
I mean Leon, right? He's the only fun one, and yes he is BAD enough to save the President's daughter. Its like asking whose your favorite character in the Evil Dead series; Ash, the one lady, the dude, or the other one lady?
RE4 is the Army of Darkness of Resident Evil games - it can't be topped and shame on you for even thinking it!
I thought Army of Darkness was regarded as the weakpoint in the Evil Dead trilogy, whereas RE4 is widely regarded as being among the strongest entries?
Also, Leon isn't Ash in that analogy. Ask anyone who the main character of Evil Dead is, they'll say Ash. Ask anyone who the main character of RE is, and they'll probably ask whether the series even has a single main character. I'd argue that the closest the series has to one is Chris, but you'd have a hard time convincing me that Leon is singilarly the main character.
Leon "Bad Enough" Kennedy. The RE4 version.
Chris is boring.
Jill and Claire are just wardrobe & haircut swaps.
I don't think Claire and Jill are swaps of each other.
Fox alluded to the idea of a spectrum, and he's kind of on the money. On one end, we have Chris - the consumate soldier, driven by justice and whatnot. Claire is on the other end - she's the most 'normal' of the "big four," and in the games she's spotlighted in, she's reguarly shown to help people younger than she is, whether it be Sherry, Steve, or Moira. It's telling that of the "big four," she's the only one that isn't military.
Leon and Jill are somewhere in the middle. Jill is somewhere between Chris and Claire, because on one hand, she's also military and this is demonstrated, most recently in the RE3 remake, where her "supercop" status is repeatedly brought up. On the other, Jill is shown to have a compassionate side as well, most demonstrated in the original RE3, mainly through her interactions with Mikhail. And Leon? Well, Leon's probably changed the most, but in one sense, he stats off close to the realm of Claire and Jill (rookie cop, wants to make a difference), then goes through his action star role in RE4, and then becomes a bit more grizzled in RE6. Close to Chris, but not quite there.
Of course, I can't call any of these characters 'deep' per se, but I think we can identify some distinct traits.