I don't think anyone is really too upset about the quirk of a 12-4 team visiting an 8-8 team. But it is at least worth discussing.
First, this doesn't happen 'every year'. That is simply not true. This isn't some massive problem, that screws up the balance of pwer in the playoffs every single year, and something must be done!! It happens every once in a while, and will happen again.
The only option, to ensure that the 'better' team doesn't get screwed in the playoffs, is to make the divisions a thing of the past. Don't have them, and seed the teams 1-6.
No more divisional rivalries. Let's get rid of those pesky, boring Jets/Patriots, Cowboys/Giants, Raiders/Chiefs, and Packer/Bear games that have been cluttering up the schedule. No more divisional races, crazy wild card chase with a myriad of playoff possibilities. No more Cinderella teams, everyone hates those stories anyway.
I am being a smart#ss here, but really, the price to have our current down-the-stretch drama, is that occasionally, a wild card team has to go on the road, and play a lesser team. Occasionally, a lesser team wins a division. Small price to pay.