I ran Eugene last year and it seems like the two water stops is a reference to the two bottle tables at ~9 and 16 they had for the the people in their elite program (similar to a big city sub-elite standard). There were water/gatorade stations every 2 miles for the first 20 and then every mile after that I believe. The cups were too small in my opinion but that is probably my only complaint. They do a great job of making sure things are as stress-free as possible pre-race which can make a big difference.
In terms of the course, I don't know how someone can think it's 3 minutes slower than a really fast course. Sure, there are a few turns and two hills in the first 9 miles, but there are turns in every course and the hills aren't bad at all. I ran NYC last year too and that is a far slower course (I think ~2 min). I don't think anyone would say NYC is 4-5 minutes slower than a place like Chicago. The weather was perfect last year and the odds of great weather are excellent that time of year with a 7 am start time. I had a great experience there are would recommend the race to anyone. There are multiple good options, Grandma's, etc, so good luck deciding and in the qualifying attempt.