Considering track record, this may well be a not-so-good suggestion. Other than that, I agree very much, especially to your first point. I'd suggest a more complex capping method than "zerg flag with many whelps". Ideas:-Make drastic changes until something good works out
Have several (e.g. two) for each flag. All items need to be placed at the respective flag (use flag with a short channel to place it). Killing the boss yields the same item for all players involved in the kill but it needs to be placed only once. Bosses can be fought in parallel and all items can be placed in parallel.A few Boss NPCs that require a group (in the range of 5 players +/-) to kill. Loot an item from each, use those to "unlock" the flags and then cap them.
This one goes well together with the "channel to cap"-idea. Have those NPCs spawning target flag channelers preferably and have them be high damage low defense type. You can get rid of them easily but if you don't close the portals, you'll probably never be successful with the cap channel.Have portals distributed inside inner keeps (e.g. two below, one on the upper level) that will spawn a group of NPCs every 15 seconds untill you kill the two portal mages keeping it open. Just to have more than two places an attacking army has to care about.