The downsides to trailers.
1. weight. (And i ride a loaded xtra so i'm not a weight wienee)
A trailer means on or two extra wheels which add weight, plus the frame, plus the bag. A BOB comes in around 14 pounds. Sure you can carry 70 pounds but the trailer is 1/7th the weight of the total capacity.
2. Handleing. At a good downhill cruise they have a habit of wandering, braking can be a little tough, if you're on a 2 wheel trailer they can get caught in the verge (the shoulder) and they track differently, still better than high loaded panniers.
3. Drag. Less aerodynamic drag than bulky panniers but more wheels means more drag.
4. Frame stress. I don't really count this one much. Arguments about frame stress points with trailers vs xtra's still forget the key point. When you addd weight you add stress. You're as likely to bend one way or another. Still, i see BOB's on carbon rear racers and wince. Definately not built for that load and asking for a cracked frame.

Still, they have their uses. I'd love to have the lockability of a BOB Coz and use it as a picnic table in camp, the removability of a trailer. For city use though i'll stick with my Xtracycle, i never forget it, never wish i'd brought it, and never run out of room. I can still lane split and turn tighter than a trailer, handle better at speed. Wouldn't trade it.