I've been to Whitefish 3 times, and we're going back in less than 7 weeks - whoo hoo!! We're taking the train from the east (north dakota), which is really convenient. There is a shuttle that takes you right from the train station to the mountain village for $26 per person (round trip). There is also a shuttle from the Kalispell airport.
I've stayed at Kandahar twice, and it is very nice - but expensive.
Last year we stayed at Anapurna, which was not ski in-ski out, but the village shuttle stops right outside the door on a frequent basis (every 10-15 minutes?). After the first day, the driver remembered where we lived, which I thought was cool. The shuttle does NOT go past every condo property, however, and the route isn't available on-line (I don't think). Many of the properties on the web site will say "walk/shuttle" in or out, but in some cases there is more walking than others.
This year we're staying at Sherpa, right next door to Anapurna. It is the only property in the village that has a pool, but many of the other condos have access to the Sherpa pool.
What I found in researching condos was that price went up sigificantly for ski in-ski out access, and for places right next to the runs. Price also went up quickly for more bathrooms. I feel that the web site does a terrific job making condo selection fairly easy, and the folks I have talked to at Central Reservations have all been extremely friendly and helpful. Be sure to ask about discounts on lift tickets, rentals and lessons if you buy them in advance.