For the most part, I use the regional Bird for my flyer. First and Second generation it was Pidgeot (Except for Soul Silver in which instead of Pidgeot it was Aerodactyl), third generation it was Swellow, fourth it was Staraptor, and fifth was Pidove. There have been some instances in which I didn't have the HM Move fly on my team, usually because there was a flying move on my flying Pokemon that I wanted instead of fly (Togekiss it was Air Slash. Swanna it was Hurricane). In those cases, I would just pick up a Pokemon that had the move fly from my PC and use them to fly to said place. It's not too much trouble, in my opinion.