Kyaikhtiyo is a 5-6 hr car ride from Yangon ... no flight there. But you can definately fly to Bagan and Inle Lake ... actually it is Heho that you fly to and then another 45 mins to the Lake. September is not really the rainy season anymore, esp if you are travelling late Sept. There will be cloud cover which makes the sky during sunrise and sunset very beautiful ....
As for overnight bus rides, strongly DO NOT suggest that ... there are no toursit class coaches between the cities, only the local domestic buses; the conditions are pretty rough and you prob would not get any sleep trying to keep an eye on all your belongings.
Anyway for a good guage of domestic flight prices ... check out the following website
http://www.air-mandalay.com/airfare.asp domestic air travel for foreigners is not cheap ....