I've ridden the eastern part, starting in Maine in early August and staying on route until Iowa. Don't let the wind be a consideration. I've read stories and talked to people heading east who got hammered with headwinds for a week across eastern Montana. So you just can't tell what's going down on the ground.
I started in the east because I wanted to be heading home with no set end date, no plane to catch. Also, because I had a wide window to plan my trip, I was able to head into the Southwest as the fall settled in with cooler temps in the desert, a big concern for me.
Although I can handle humidity, it's not my favorite by a WIDE margin, so I would personally try to minimize my exposure to the heat and humidity of the East/Midwest, which is hard to do when a typical crossing takes about three months.
Another consideration (I think others will agree) is that the hardest riding is in the East in terms of climbing--some really brutal grades. Hitting these first on the tour, fully loaded, is a bit of a shock, so be well trained in climbing if you start in the East. Don't be shy about walking and he bike a little here and there. I did this a couple of times and found that others ended up doing the same--even after riding from the west coast. It's hard to overstate how steep some of those roads are in New England--yikes!
Ultimately this will be a personal choice, pro's and con's either way. Because I was familiar with the mountains of the West, the wild terrain of New England was my favorite part of the ride.