The downsides I've had are that the tube freezes and if you're backpacking with a full pack you often have to unload a portion of your bag to refill it. I've seen the Sawyer "system" where you can flip a valve and force water back into it, but I highly doubt it would be as easy as shown. Also, a Nalgene works really with with a UV style water treatment.
Actually, filling a bladder with a Katadyn filter is about as easy as it gets. Drop the pack , hook to the hose, and pump away. Never have to remove the bladder.