What I would like to see happen.
As you level up (maybe every 10th level) you get an extra alliance flag.
So the more you play the more you get. This could be quite fair as both pay to win and free to play players would have an equal chance to get more flags and having the increase at every 10th level means that you wont have a very drastic difference in flag numbers between new and long term players.
The more time you play the more you get.
1-9 = 3 flags
10-19 = 4 flags
20- 29 = 5 flags
30- 39 = 6 flags
and so on.