I'm sick to death of farmers ruining everyone's fun, but I think a couple of simple changes could solve the problem for everyone.
Step 1: Set a maximum XP/Influence cap per mission
I know, it sucks for those of us who play by the rules, but there's bound to be some way to figure out what the average XP is for a standard dev-created mission, and then set the bar at maybe 10% above that. People may still farm because the "prey" is easier in AE, but it could sour the milk enough to get people back out into the sewers and Perez Park if all they want is massive mobs of enemies and XP/Inf.
If players still feel gypped by the lowered XP/Inf, perhaps the excess can be converted towards tickets instead.
Step 2: Grant Architect players extra debt protection
I can't remember whether this is in place or not. If it is, ignore me, but since all AE missions are simulated, it stands to reason that "dying" in one shouldn't count against you quite as much. This would be a good counterbalance against the XP/Inf penalties above.
Step 3: More slots for veterans/money!
At this point, I desperately want to make more missions, and I'm willing to do almost anything short of buying a second account!!
The Hall of Fame and Dev's Choice are excellent ideas (if for no other reason than monitoring popular arcs is a good way to weed out farmers) but it shouldn't be too difficult to add one extra slot for every 6 months you've been subscribed to the game, or $9.95 for 3 additional slots with an upper limit of 15.
After all, most farmers aren't going to care about additional slots, and they definitely won't want to pay for them. What's the difference between playing 3 arcs that are exactly the same or 15 arcs that are exactly the same?
More slots for people who want to be creative = more creative content in the game = the ratio of good arcs over stupid farming missions goes up!