Some great advice above. My only suggestion for Denali would be to avoid the tour buses. SuperCrewBear mentioned the Wilderness Tour (Tundra Wilderness Tour - TWT - I assume). This is a tour geared 99% toward cruisetour passengers. The buses pick up and drop off at the hotels, the tour buses usually fill every seat. But the transit shuttle buses depart from the Denali Bus Depot (no problem getting there with a car). The transit shuttle buses travel along the same road, make the same rest stops and the Eielson shuttle actually goes 4 miles further than the Tundra Wilderness Tour to a really nice Eielson Visitor Center. Plus, the transit shuttle bus costs about 1/3 the price of the TWT. Transit shuttle buses always depart with a few empty seats so they can pick up people along the way. That is another reason to take the shuttle buses - you can get off to walk along the road, hike or just spend more time at the Eielson Visitor Center if desired.
I agree with you 100%. If we ever do this visit again it will be on the shuttles. As you said, the seats were all full - so crowded. The price difference is significant - at the time we didn't know any better. The shuttles have drivers that I've heard do a great job of narration (like the more expensive option) plus they also stop when wildlife is spotted. The shuttle is definitely the better choice. (Take plenty of snacks and drinks.)