This thread may be useful:
http://www.whiteblaze.net/forum/show...&highlight=PCT
The short hand description is, in general, the PCT is logistically more difficult and the AT is physically more challenging. I'll add to this nugget that this thought is generally true for people new to long distance hiking.
I think that the AT is perceived as physically more difficult is that because many people new to long distance hiking are carrying heavier gear, are not in the best physical or mental shape for ld hiking and do not have the experience that veterans of long trails may have. So the first long trail is perceived at the most difficult physically.
Parts of the AT are indeed more physically more difficult than the PCT (the Whites and the Mahoosucs come to mind), but overall I think the AT is not that much more difficult than the PCT imo.
If you are the type of hiker who is not mentally geared for doing more than 15 MPD and likes frequent town stops (and likes to get in 'trail shape' on the trail), then the AT is perhaps the better trail. Frequent towns and very conducive to a 12 MPD or so pace.
Based on your posting, you are probably in better shape than most people starting a long trail. I do not know how much experience you have outside of weekend backpacks, so you may want to do a two week backpack somewhere to get used to the mind set of thru-hiking. Resupplying, being out in all conditions, pacing, etc. The Long Trail in Vermont is a good trail to try out ld hiking (if with harder grades over alll than any of the trails I've done). If you want a challenge that is local, try the Cohos Trail.
(At 160 miles, perhaps fits your schedule more, too)
FWIW, many people say the PCT is, in some ways, a better first trail. Well graded trail, good views, logistics aren't too bad if you are willing to change the "more camping, less hiking" mindset that is common to backpacking.
As for a 90 days pace....difficult, but not unheard of. You may want to
read Suge's journal for what a hike of this pace entails. Most, but not all, hikers on this pace have done a long trail of some sort previously.
Finally, light gear is not just for tall, skinny guys. It is also for lazy guys like myself who are built more like a dockworker than a distance runner.
I can haul ~50 pounds of food, wine and gear to a hut on skis. Doesn't mean I want to do it for 4 mos.