This list is a work in progress - as I write it has yet to unveil the top 14 characters from each company. I.e., it currently lists the 15th to 50th most popular characters from Marvel and the 15th to 50th from DC, based on votes from "nearly 1400" fans. The list will reach completion during the remainder of September.
I don't know all that much about DC, though it's obvious that major characters such as Superman, Batman, Wonder Woman, the Joker, and Green Lantern (the more popular incarnations of the character, since one incarnation is on the list already at 23) are still to come in the top 14.
I know more about Marvel, so let's play a game of who will be the remaining 14 characters. I predict that it will be something like the following group of characters, in something like the following order:
3. Captain America (Steve Rogers)
4. Iron Man
5. The Hulk
7. Doctor Doom
9. Professor X.
11. The Thing
12. Mary Jane Watson
14. Doctor Strange
I can't immediately think of any other characters who could turn up in the top 14 and are not already listed from 15-50. But maybe I'm forgetting someone. As mentioned below, the Wasp may be an outside possibility, but I kind of doubt it. The same goes for Juggernaut.
I hope I haven't named someone who already appears on the list somewhere.
The list so far doesn't contain many villains - I notice Loki at 45 and Thanos at 44. I suppose it's possible that the Red Skull will sneak into the top 14, in which case someone I've listed above won't be on the list at all. The three villains whom I expect to make the final 14 and possibly even top 10 are Doctor Doom, Magneto, and Galactus ... all of whom are among Marvel's most interesting and iconic characters.
The list is also light on for female representation. In fact, this is culturally and commercially important. I've guessed that Mary Jane Watson will make the list, maybe just outside the top 10, but perhaps she won't be there at all. She has a large fan following, but maybe she's not an obvious character to vote for. If, in the end, she doesn't appear at all, the highest ranked female character in the voting will probably be Emma Frost at 17. And I just can't see any female character appearing in the Marvel top 10.
I'm sure that Marvel is concerned at its inability so far to create truly iconic female characters, but this is an area where renewed effort is needed - for the health of the industry apart from anything else.
The female character that it tends to push most, Ms Marvel, is languishing at 29. A number of prominent female characters from X-Men are around 20. She-Hulk comes in at 26, and there's only a small smattering in the 30s and 40s. Some potentially great female characters such as Polaris, Umar, Magik, the Enchantress, Medusa (but her husband, Black Bolt, isn't there, either), and Moonstone don't appear at all so far ... and are most unlikely to be in the top 14. Even the Wasp isn't there, despite having been an Avengers leader, though I suppose there's still an outside chance that she could appear somewhere in the top 14.
Hopefully, as it were, this list will look different in a decade with the recent creation of several potentially interesting female characters, among them Hope Summers and Finesse, but it remains to be seen how much popularity they can gain.
I don't see any female villains, unless you count the Scarlet Witch (which I don't). Some of the female characters (such as Rogue, Emma Frost, and the Black Widow) are reformed villains, but it looks as if Marvel doesn't have a real female villain (even as real a villain as, say, the morally-ambiguous Galactus and Magneto) who can make such a list. The nearest thing is Emma Frost, who is still presented as snarky, unscrupulous, and not a nice person, but as having reformed a long time ago and pretty close to totally.
We need some villainesses to get more prominence. Marvel is doing a good job with Moonstone, but she could be upgraded in importance even further - she's a potentially great character. The Enchantress is another who could play a bigger role. (To be fair, some important male villains also look like not appearing on the list - the likes of the Green Goblin, Juggernaut, Dormammu, Absorbing Man, and Doctor Octopus.)
Edit: A few people - here or on Facebook - are saying Mystique, and I think that's probably right. I'm kicking myself for not thinking of her, especially after complaining about the relative paucity of female characters. Mystique is very popular, especially from the X-Men movies. That would give us a female supervillain, and possibly the highest ranked female character in the Marvel list. It would also mean that at least one character on my guess of the final 14 won't make it at all ... and I suppose Mary Jane Watson is the most likely of them to have been overlooked in the voting.