The cover 3 is normally fine. We are currently without THE GUY that normally can call out what an offense is trying to do in Kam. What's absolutely true though, is that the cover 3 defense is inherently weak against the short pass. When Kam is in there, he helps mitigate that due to his understanding of offensive formations and angles. Cover 3 still has that weakness though.
Don't be a fan or not a fan of zone though. Zones have different emphasis and try to accomplish different things. We run 3 deep, 4 short, thus putting emphasis on deep coverage, which concedes some short passes. If you're worried about short passes, you go cover 2 where you have 5 short zones and only 2 deep. We don't run it that often, but we could if we so choose.
One of the problems with man coverage is that if one of your guys loses, then he's running a lot more free if he can get some RAC. Often you still have two safeties over the top or at least one, but they still have to track that and get there.
Every defense has it's weakness, we just don't varry a lot.
Speaking of variation, the cover 3 has quite a few variants in it's own.
All last game we went with the same exact cover 3 each time. Both the MLB and WLB were in short zones. We have other styles where Kam will come up and take Wright's short zone (my favorite) and Wright will bail to the flat. There are robber coverages where the safeties disguise swapping deep for short or deep for flat. This is where you'll see Kam bail deep and Earl come up short. There are also some others, but most revolve around Kam being able to play mulitple zones, from deep to short to flat. He's he real cog, IMO.
One thing about man coverage is that if an offense identifies man coverage, particularly with pre snap motion, you'll start to see rub routes that you just can't stop. Vets like Brady eat it alive.
There is always a kryptonite. I'd like to see better, more appropriate mixture of play calling based on down and distance, but I thought Richard had a lot of learning to do last year. When inside the 10 or there abouts, I'd like to see more cover 2. That Cincy game last year was proof of it. Kam or Wright releases the TE in their short zone and the FS or CB is too far away to get there and they get two TDs. The spacing for the red zone is better for cover 2, IMO. However, if you make a habit of it, other teams will adjust...such as running a play where you send your slot on a post pattern between the safeties and send your wideouts on flag routes away from those same two safeties, They'll have to choose and they can't cover all 3.
There's always a weakness.