Why? Right now flag is just useless object in gamedesign, you could click on it and nothing changes. It's only obstacle for vehicle (hi pathing problems in some maps) and infantry.
Such change will increase value of "ambush" troops, like partisans, storms and e.t.c, they will be do what they must do - break enemy supply lines. Also any tactics with carrier vehicle wil be more better and backsitting style of gaming will be less pleasant. And of course "high risk-high reward" rule working the best in this case.
it will just result in running around map and cap/decap orgies. play dawn of war to know what i mean