I really don't think crowd congestions will be a factor for you. With a 3:28 that will put you in Corral A. That is where I was in both 2006 and 2007. Both times I was across the start line in 10 seconds or so. It is pretty wide at the start, so you can spread out. When it narrows you will be well out of the way. I ran a 3:34 last year and hung well with the 3:20 pace group until that sun came out and cooked my splits about mile 20. My feet felt like they were 130 degrees. I was really bummed by my time.
The weather is the big factor. You never know. 06 weather was wicked cold at the start (32f), but turned into beautiful cool running weather a little later. Last year was scorching hot (87F and humid). Go figure!
I would consider the course pretty flat, but that means no speedy descents. So consider that a pro or con however you like.
The other factor that could influence your decision is crowd level. You really only get the crowd influence through the parks. If you run like me, then low crowd level is a plus. I always feel like I have to go faster when people are cheering me on, and that totally blows even splits.
I am skipping WDW08 and am going to try to run Marine Corp, if I can maintain a steady training schedule over the summer. If not I am going to run Kiawah, SC in Dec. That race is really small, 2 loops, totally flat and fast. I need to run a 3:15 to BQ. I am also stepping up the training and am going to try Pete Pfitzingers 18 week 55+miles. He does a lot of speed work, lactate threshold, VO2 max runs. So we'll see if I survive training!!
Best of luck on your decision. Just being at Disney and running is pure magic.
Dave