I am not even sure there is anything to be fixed. The flagship allows for a faster game opening, since it is an awesome tank. As game progresses its relevance at the front line diminishes, and then it has to be guarded to avoid losing the game.
It make the game start at a faster pace, and makes the dynamics more interesting, since different strategies are needed at different stages of the gameplay.
If anything, making the flagship more maneuverable and faster would help its survavability in later stages, make it a runaway coward. But I'm not sure it's even necessary.