Here is my thoughts on Zerg game play.
Zergs can indeed be a problem if the game mechanics are poor.
Big guild zergs do have numbers, but they also have very bad players. If you look at probably the best created zerg warfare game we know about, its probably Archeage, the game sucks, but when it comes to pvp fighting, the zergs do lose to much smaller good armies.. I think we at times we had 40 players vs a 200+ zerg and we wooped the 200 regularly. Not many games this will happen, in fact I know of none other...
I believe the game design here allows only 150players per "guild"? I could be wrong as I read alot of gaming stuff daily but limits like this are helpful as there
are some crazy large multi-gameguilds out there that can really cause issues. There are issues for guild limitations... such as friend play, oh you cant join this guild, cuz we are capped at 150. Okay, now we have another issue, are players going to leave guild, to play with friends, sometimes yes... this is catastrophic for many... next you have alts... this game and its vessel system might not have alt. but now, you have limits and you have big players with 2 accounts for hoarding, muling, etc, this takes up slots. But with 750 you have issues, of guilds getting to powerful, funneling all their grinding can give too much power and control. able to self fund, control markets, take more land than others and so on...
llegiances were born to stop this, allowing small guilds to unite,, (I think that was the plan) Not sure if good or bad, have not seen great scenarios of allegiances. I did play WAR, which probably was the biggest allegiance game, They were all run by corrupt large guilds emphasizing power over everyone with strict rules and powers to even kick individuals out of other guilds, if those guilds wanted to stay in the alliance... I single handedly warred and disgruntled on a large guild watching them do some really hooligan poorly made socks to single individuals that affected them and their fun in real life for no reason whatsoever. Seriously, some shady epeen poorly made socks goes down in allegiances. .
Zergs do have easy control of area's/content. This brings in the game issues.. Players not in zerg armies could never grind for gear in these public areas because when they were grinding they didnt have the power of their army behind them. But the sheer force of zerg guilds, made it simple for their own player base to grind, as the numbers game gave them the grinding area. The end result when this happes, is that you feel your gameplay is halted. Your a disgruntled off player who can't get the needed tokens to buy the sword to move forward. Next the bad players have the gear, which now your fighting against geared nubs, who now have no chance of losing, as long as they mash a button. Which is a reason that game was abandoned quickly. Cash shop lottery purchases anyone? No thanks...
The next issue is instanced battles... When you have people, one this is obvious, the simplest path to achieve the rewards (note rewards, not victory) will be taken. This is why most games fail in PvP.... SWTOR anyone? Everyone ran in a pack to the next red enemy and the lagfest of who can get the casts in and which team has the best video cards and/or graphcs turn down wins the battle. No one ever played objectives, sending a party there, there and there at the same time. Anyone care to run in a circle and press heal in Wildstar? Wildstar shows off piss poor thinking and some good design at the same time... some places had multi attack, some had the circle jerks. I think they abandon the multi attack areas for the shear sake of supporting casual gameplay. Casuals need to follow carrot on a stick, they can't think in real time, so if you split them up, they get crushed, but this is what is suppose to happen, but wait, we can't have our casuals losing comes into game design logic? not sure, but seems like it.
To do zerg gameplay right, you need to force teams to be here, here, here and here, at the same time and I guess make it obvious. I think some WoW battlegrounds do this okay, but not great... I think the classic ones you recall and liked, all share this mechanic.
Lets look at simplistic zerg games.. H1Z1 battle royale.... Game is never played as it probably was designed, all man for himself, people zerg to the end, and share the victory. so much they changed the game design to be team... Game always ends with you running to the final mountain only to realize, its you on 5, not you on everybody.... (again showing how people take the easiest route to rewards) The whole game is now alternated and you just lost that whole "hunting, in the bush experience, immersion" now its bubble gum skipping hop-fest to a one time standoff of who has the best guns and hacks. Yes, trust me, they see you on radar while your creeping thru that grass for 1800 meters. your better off running at them in a straight line and not giving them time to communicate, cuz they are not the best skilled players who can react, they're usually jabbering some nonsense on their skype call (okay enough of my bashing h1z1) ;P
there's no simple answer to the zerg, only experience in design to help alleviate your game design principals, The only advice i can give, is that winning, (not controlling) and make winning a skill to achieve to get resources is the only route to take, and other ways to get those resources are available as a time sink.
Obvious things such as debuffs for being overpopulated, are thoughts... or buffs to opponents, are always helpful to deter mindless zerg tactics. But if larger guilds should lose more when LOSING, is a good way to look at design as well. And make victories for the smaller guilds more tantalizing.