I had to read the comments here to see why on earth JJ is winning by such a huge margin. No help, everyone who bothered to post a comment has been on Joss's side. I agree with all of the above, Joss Whedon has a frightening talent for storytelling, creating the most 3-dimensional characters I've ever seen on television, and playing with the spectrum of human emotions effortlessly. Buffy, Angel, Firefly, Serenity, Dr. Horrible. 'Nuff said.
J.J. has had barely anything to do with Lost since the beginning of the first season. The vast majority of his career in general, though most of it has entertaining, has been cheap hack work. Joss Whedon is a man trying to work out serious issues and portray something about the human condition and does so by using the devices of his genres. JJ tosses an idea here or there but more often than not he seems to just want to see shit blow up. He is a talented versin of Michael Bay.
Joss just know how to put every human emotion in his series and make us join with the characters. Well maybe not so much yet with Dollhouse, but Buffy, Angel, Firefly and Dr. Horrible kept me coming back because I connected with the story. I did love Veronica Mars and am enjoying Fringe, but Joss has me watching what ever he does. Kind of like James Marsters, if he is in it, I am there. Spike was the best character ever on TV and for me Buffy was the best series, so that puts Joss way ahead.
Here's what puts Whedon over the edge. While JJ is a prolific producer of TV and film geekery - likely moreso than Whedon - its Whedon who manages to embrace material and mediums out of respect for geekery.
For example, any geek will tell you that Veronica Mars was a tremendous show of both JJ and Whedon-level proportions...but it was only Whedon who embraced it and paid it respect by appearing on the show in a cameo...
Beyond that, his ability to tap into the most geek-friendly mediums like the internet (with Dr. Horrible) and especially comic books (having continued his own TV series in comic book form and let's not forget a brilliant run on what is the holy grail of geeks - the X-Men - in his Astonishing X-Men comics), it's clear that he has his finger on our collective pulse.
While most geesk will love JJ and anything he crafts on screen, he has a long way to go to establish the life-long and unwavering loyalty that Whedon has earned among our people.