This is a good list, but I've got a slightly different take. Like you, I'm going to ignore/omit obscure and/or inactive characters.:
1)Iron Fist: The one time he and Shang-Chi fought (Waaaay back in Deadly Hands of Kung-Fu), Danny looked like he had the edge (though to be fair, the fight didn't have a definitive ending, it was a classic 'team up and fight the bad guys instead type of thing). Plus, with the additional training and insight into the Iron Fist powers he got from Orson Randall have probably elevated him to the top spot in the mainline Marvel U for the moment.
2)Mr. X (Thunderbolts): Has supposedly mastered every martial art on Earth and is, per the latest issue, currently adding the Kree and Shi'ar martial arts to his repertoire. Could probably mount a serious challenge to Danny.
3)Elektra: Martial Arts virtuoso w/mystical ninja abilities. 'Nuff said.
4)Shang-Chi: Best pure martial artist on the list.
5)Captain America (Steve Rogers): Brilliant unarmed combatant, but largely self-taught.
6)Gamora: The closest thing the MU has to a Cass Cain type.
7)Wolverine: Has had lots of quality training, but also prone to undisciplined brawling.
8)The Gorgon (Wolverine/Secret Warriors): Chief assassin-type dude for the current iteration of Hydra.
9)Black Panther: Along the lines of Cap, but not quite as good (I categorically deny the existence of Hudlin's stuff).
10)Karnak: Well trained and highly disciplined, with powers that should theoretically make him even even more badass -- yet seems to get pwned on a pretty regular basis. May lack heart/fighting spirit.
11)Daredevil: The second or third best pure martial artist on this list, but 'only human'.
12)Winter Soldier/Captain America '09: May not have realized his full potential yet.
16)Taskmaster: Mimicked the bulk of his skills, as opposed to 'earning' them the hard way -- which, IMHO, would out in a fight with a top level combatant.