How about this for MNF?
Have all Monday night games be divisional match-ups between the 2 top seeded teams in each division. The following week, the same teams play each other Sunday 1pm. It should initially be the top 2 ranked teams from whatever division each week (based on final rankings prior season). Playing the same team the following week would eliminate the "short week" advantage/disadvantage. It may add some excitement to the match-ups also, knowing the two teams will be playing each other 2 weeks in a row. Interesting effect on game preparation and adjustments.
For example. Patriots win the title and are top seeded. They would automatically get 1 MNF Home game against the second seeded team in the division. The following week, those teams would play each other again Sunday 1 pm at the second seed team's home stadium.
Scheduling committee would have to decide best match-ups to schedule which weeks. There are other details that would have to be ironed out. For example, 2 overall high seeded teams in same division. Would you give the second seeded team a home MNF game against a lower seeded divisional opponent? Maybe not cause then they'd have 2 MNF games to the top seed's 1.
I suppose the downside is you wouldn't be able to get some of the exciting cross-divisional and cross-conference matchups.
I don't think it's possible to work anything out for Thursday night games to mitigate the advantage/disadvantages unless you try to work the bye week schedule around the Thurs night match-ups. However that would limit or completely eliminate the ability to swap out games mid-season.