Balance is never easy in MMOs, which is why Bethesda is putting a lot of effort into making sure that it's Elder Scrolls Online factions aren't weighted in favour of one or another. Of course, with big battles being part of the game's future, there also needs to be consideration for how do you balance overpopulation in one army or another?
Don't worry, Bethesda is way ahead of you.
"There are alliance population caps per campaign to make sure one alliance doesn't fill up a campaign entirely," the studio said in a recent QnA. "There are also scoring incentives for alliances that are tailing behind when capturing resources and keep, from the winning Alliance if the score is imbalanced. You'll get more points by taking keeps and resources from the winning alliance and holding your own keeps, helping you catch up in the overall score. Lastly, keeps can be captured with smaller groups than you may expect, so even under-populated alliances have a real shot at claiming the throne."
Not all battles will be large scale though. A lot of quests will be designed to be handled by individuals or small groups, many of which will put you in opposition with other factions - so simply questing around can put you at odds with a real enemy player.
"There will be lots of chance encounters and roaming players to kill in Cyrodiil. Many of the quests from towns and from alliance entry locations are designed to send you into enemy territory. If you’re looking for a fight outside of large-scale keep battles, there's a good chance you’ll run into enemies near Chorrol, Cheydinhal, Bruma, Cropsford, or Vlastarus."