The way how sieges have been won so far in CCNet have been through; Night Capping, Player Spamming, and most importantly Suprise sieges, which have but few Counters and makes a lot of people want to quit the server because of these, Cancer, server destroying, and absolutely 0 skill metas.
It doesn't require skill to Night Cap, it just requires having no life at all.
It doesn't require skill to player spam, you just need to bring on a pvp clan from some other server.
It doesn't require skill to Suprise siege, you can probably catch an entire nation off guard at the worst possible time ever.
My suggestion. Is that. No matter how many people you have capturing the banner, you get points based on just TIME.
Not TIME & PLAYERS, just TIME. This would make it so that, if any one side didn't have a lot of players to cap with, they could still make a difference because of time.