Aaron, I've only done it ten (it's the only thing I have to sort of brag about) times so my information might not be the best but the permit thing is kind of a, "Duh", or "Doh" . . . you need a permit for just about everything, no matter where you come in. It might be easier to get a permit for the JMT from Cottonwood, simply because it's less trafficked in the summer than getting a "go" from Whitney, although in my experience, you'll do fine just showing up and being able to wait around a day in LP, should you not get in on that days walk-in permits.
When the JMT was built and christened, doing it from south to north was supposedly the official way, but hardly anyone does it that way because . . . for one . . . It's better and easier to start in Yosemite and gradually work into the altitude thing––if you come fresh from sea level and jump onto the JMT at Whitney, your first couple days are probably going to kick your ass and should you take a longer time to acclimate, you might even find yourself getting burned and off the trail.
But the biggest reason, in my book, for doing it north to south is, that you've chosen to do this grand adventure.
If you start at whitney, you've already kinda done the best part of the trail, which again, I think, would be the BIG PASSES . . . north to south it just keeps getting better and better.
Lots of people only do it once in their life and how many of us ever walk 200+ miles . . . and generally we celebrate triumph/accomplishment by being, shall we say, on the top, the summit and so on, so . . . again, for me, I'd rather end a trip like the JMT by sitting up top of whitney and taking it all in. You finished––you're at the top and all you have is a short walk to the portal, burgers, beer, (watch out for Doug's pancake though!) and a ride into Lone Pine where you can soak your aches away in the hot tub at the Dow Villa . . .
. . . of course if you go from south to north you get to finish, if you go all the way into the valley, by walking down into the crowds of people in clean clothes and screaming teens and cars all around and where's the triumph in walking down into Yosemite Valley. oh boy. Sure you've finished the trip and all, but . . . there's no summit to sit and look back at and there's no hot tub
. . . anyway, I'll shut up now.