Balanced in what way?
In a way that it's neither too easy nor too hard anymore. You don't absolutely have to bring in a massive horde anymore (as it was with 100% and no flag), nor 2-3 bombs in the middle will bring it down to 50% and capturable status.
Changing the difficulty to either extreme has a great impact on game dynamics and player motivation. Too hard and the map is getting stale quickly,defenders have a big advantage, lots of people frustrates cause they hardly have the chance to "win" a fight for a base anymore. Too easy and bases will get rolled in quick succession with little chance for the defenders to muster a defense in time. Lot's of frustration again, this time on side of the defenders, with one result being a "I grab your base while you grab mine" kind of gameplay with little actual combat.
Keep in mind that Hitech said about the new towns "It was never intended to make captures harder". But they actually did, by having much more buildings, more dispersed, and by making the identification of individual building status much more difficult.
The flag is a toll simply introduced to correct that higher difficulty.
May I add that we still have a base capture rate much lower than we did for many years in Aces High, but that's to a big part also a result of the new off-hours arena setup.