I wrote a long thread about this a while ago but I can't seem to find it.
I agree with redeye that duty rigs are the solution. I think pilots should get per diem for all time away from base. I think pilots should be paid their hourly wages for flight hours. I think that every company should have trip rigs that encourage the company not to waste the pilots time.
But here is my solution. Pilots should be paid for time spent preflighting/checking the weather/ anything else that involves working prior or after the flight. Lets say you need 45 minutes to check the weather, preflight, etc... For each leg you fly, you should be credited this time at flight pay.