you can just say flyers can't capture the objective or the one with the most points within a distance to the objective.....so a flyer not worth a lot of points couldnt even have a chance to get the objective from the opponent with some nice infantry close by.
Best yet, just say no flyers for the game.....it is a scenario after all and what better way to beat boredom but by taking certain stratagems out of the equation. also, no cavalry or monsters etc. etc.
I love scenarios, I try to play with the random scenario generator all the time now. When me and my brother can nail down some time to do a full campaign with mighty empire tiles I will use it for every engagement and use everything, even the weather, which would affect missile troops and flyers.
Someone always feels left out I think by being forced to play as the underdog but oh well.
My wife likes being a "gamemaster", placing the terrain and what not. I will have her put in random troll encounters in the map as well or even use chaos marauders as bandits or something like that "evil men", that sort of thing. Someone usually gets screwed over but its fun.
I like the objective scenarios the best.