Yes, I always recommend the shuttle to Eielson. I can not see paying 3 times that price for the tour bus, when there is not much difference, except the box lunch. I have never been on a shuttle bus where the driver wasn't very informative. But if that is what you want- go for it.
Some people don't know the differences with the buses, just be informed what they are.
Anyway- have plans in place- if you don't want any of the Skagway activities- take the ferry over to Haines- consider a tour with Yeshua or a great rafting with Eco Orco. But be sure to at least get to the free Park Service visitor center in Skagway. http://www.nps.gov/klgo/schedule.htm