I see several problems with the flags as they are right now.
It's an all-or-nothing game, which is a bit restrictive.  All 4 strat battles I played today (I was both defender and attacker) ended in less than 15 mins.  Most were 5-6.  The flag gets capped and its over.  I'd like to see multiple flags and multiple spawn points on the map, more of a Battlefield series style game mode.  Having maybe 2 spawns on a village, 3 in a city, and 4 in a castle would be ideal I think.  
Secondly, its very confusing shutting the flag on/off.  It needs to be easier to see and select.  Also, as defender, you can't tell if the flag is capped or not.  Adding a toggle-able HUD icon for both sides would be nice.
And I think cav can cap flags, right?  That's unlike all other flags and usable items in the game--I was rather surprised to see that. edit: nvm its a bug I suppose