The only negative scenario I can think of by removing the flag indicator is if someone runs off with the flag, teehee, and drops it somewhere obscure, and doesn't tell anyone, or people simply forget where the flag is and have to wait for a return. I doubt this would happen often though.
Oh, and trying to tell new players where to go in AvD instead of just saying "go to that floating circle" (though, on the flip side, I think it's pretty obvious where to go in most cases, and shouldn't be hard to explain).
Teamwork would definitely increase, as would the need for voice comms, and more strategic capping could open up on a number of maps as a result.