Well, as I've played my fair share of jailbreak, here's my input. I believe that the main purpose of pyro, soldier, and demo are killing rebellers. Whilst having a shotgun secondary for pyro would allow the class to kill specific people, the flamethrower is useful when dealing with day rebellers. What I call a day rebeller is someone that runs off during the round and tries to get ammo, rather than it being someone who just didn't do an order. Pyros and the other AOE classes allow the blus to stay safe when there is a day rebeller either off in the distance, in armory, or with ammo ready to kill blus. Their AOE may not be good for specific targeting, it's good for rebellers. Another point I should add are scouts. Scouts are a pretty common red choice, and really only have 3 and a half counters when their running or up close and personal.*The soldier, who has good damage and rocket jump mobility is a good class to kill rebelling scouts. Another scout, who could chase down the rebeller. The pyro, who has a good AOE weapon and maybe a flare gun for distance engagements. I count demo as the half because his range isn't great and his mobility costs his health. With 2 and a half of those options removed, having a team of scouts is not optimal. So, I say keep the AOE classes. Of course, this is all opinion.
*Note- There were 2 other classes that came to mind; Sniper and Heavy
I don't say these for the following reasons
Sniper: Only a good counter if you can aim and hit a running scout
Heavy: Good at killing the scout in close range, but lacks any medium to long range potential
*Note 2- I like the idea of a motion sensor for engie