Blizz seems to have heard the thoughts of the community, and has recently said that they are going to make skill swapping an in town only feature. Previous to this change, they said they had already considered doing it, but it just felt bad overall to have to port back to town just to switch skills and port back to the action (and I sort of agree with that). They also said that this recent change is just where they are at with it right now, and is not the final decision on the matter.
So here's my idea: swap skills not only in town, but at the checkpoints in the field. Maybe add some kind of visual marker to the checkpoints so players can go "Hey, a checkpoint stone/pillar/cow statue! Maybe I should swap out X skill for Y skill while I'm here". That way, you won't be able to abuse on the fly skill swapping, but also not have to be bothered to stop playing, channel your recall stone, swap your skills, and port back to the action just because you picked up a new skill or rune. It might even give you motivation to keep going forward! "Oooo, a shiny new skill/rune! Let's hurry and kill all these demons so I can swap them out at the next checkpoint!"
Probably not the best solution, but if they are STILL trying to figure out exactly how they want to handle skill swapping, a suggestion is usually not a bad thing. Maybe it'll spark an even better idea from someone else.