Low pop bonus should just be removed from Cyrodiil.
Also make night capping far more difficult and time consuming.
The Imperium of The Eagle and Crown Royal guilds destroyed bothe the Ravenwatch and Blackreach campaigns in Cyrodiil with their gating both other factions every night after zerging the entire map (thanks to the tank meta and Scribing allowing everyone to stack shields & heals).
ZOS could do something like have guards get logarithmically stronger and harder to kill when there's a significant population difference such that the faction attacking the keep has a significantly higher population than the faction that currently owns the keep. Make it not worth the extra hours of time it would take to run the whole map overnight. Make it impossible for 2-4 people to turn the whole map one color when no one else is really on.
And make the rewards for winning a campaign actually worth it. Right now, who wins a 30-day campaign really means nothing. The rewards of first vs third place are negligible.
Getting gold jewelry to sell used to be nice for being in the top 100 or 50 of the campaign leaderboards for your faction. But now those rewards too are useless since Chromium Platings drop like candy from daily crafting writs with the new jewelry crafting system.
I know it's hard to believe but that's another reason why Cyrodiil pops have fallen. A not insignificant number of people used to PvDoor a lot to grind AP to get up in the leaderboard so they could sell the gold jewelry they got as rewards. They no longer do so because gold jewelry has no distinct value anymore.