1. Unclear rules in zone control are problematic.
We don't care about capped zones and win/lose status of ZC - it doesn't give anything compared to losing your gear. Our only goal of ZC - is elimination of the enemy. But if we are 6 came to the zone first, enemy are 10, they took 51 score over our 50 - now they expect us to rush to fight for the zone. Won't happen as it's not worth it.
Making scoring system balanced for amount of people in the zone from sides should help it, but taking into consideration alliances between 2 factions - it won't help completely. It will be sensible to split your party in 2 factions to get more score.
2. No communication between factions makes you stay in the zone for 20 minutes having no clue if anybody will come to fight. Cross-faction communication won't solve it completely, but at least will help it. As well as I don't see point in faction chat, when everyone has a spy.
3. ZC 20 minutes timer. 20 minutes of wasting time without a reason if nobody comes. It could be fixed by ZC registration system (3-5 minutes after start to register you response group, if not, zone considered to be capped, if yes and didn't come - penalty)
4. 1 person ghost capping. Decrease the score for those, who left the zone to negative values.
5. Abusing faction system. While standing 20 mins for nothing you can bring alts and kill them getting around 2000 caps.
6. Capping the zone makes no sense. You can always bring an alt in enemy faction and but from their shopkeeper. I'd suggest to have the system based not on capped zones, but on overall ZC score for the last week. So if everyone fights hard, everyone gets the best loot in the shopkeeper. Giving the best loot only for those who owns the zones makes no sense as well.
7. Reward for ZC being less stable and less profitable than assignments. If it's risky, it should be much more than assignments, although need to fix exploits first.
8. ZC party is more hobo than pve folks. There should be a system, based on your score in the ZC, giving you not caps but some kind of spendable points to buy the best (or the cheapest) equipment, in the same time not accessible by people with millions of caps from assignments. Best and cheapest equipment should be given only for ZC party.
9. More maps for ZC. There're many cool maps unused. Adding all maps for being Zone Controlled for the sake of variety should be cool. Could be done with "Soft Zone Control" system, letting blue suites to come across.
10. Support roles ZC reward. At least buffing medic reward. Could be extended by reviving, smoking, even tanking? Looks abusable (not much different from current one).
UPD: even time spent in the zone for very low amount of points.