As others have mentioned, flying into Kalispell is very expensive. I did this trip in Mid July a couple of years ago and flew into Butte and out of Bozeman for about 1/3 of the price of what it would have cost me to fly into Kalispell. The rental car was also cheaper (and was not charged the usual one way fee).
Since we were driving from Butte, we started with the Two Medicine Lakes area, then up to Many Glacier, back down to St Mary Lake, and finally headed west via the Going to the Sun road to the Lake McDonald Area. Top trails were Grinnell Glacier (did it on July 15th and it was the first day the trail was 'officially open' - still had to hike through A LOT of snow to get to the glacier), Iceberg Lake, and the Highline trail (loop).
From the Lake McDonald Area we drove down to Missoula and then Yellowstone (the reason why we chose to fly out of Bozeman). The drive is very easy, so you can also consider splitting your time between the 2 parks.