So why are they running instead if playing?
Because they don't want the punishment of being sent all the way back to the tower and have to waste another 30 min of their day bored to death on auto-pilot just getting back to where they were.
And that's if the one fight on the map they've found hasn't already dissipated by the time they get back.
3 sided war created more frontage to spread the fights out across and many times the one good fight on the map will be where a third of the players can't get to because they don't share that front. 3 sides are great with 500 players to prevent a cluster-fek. With low numbers it makes it harder to achieve critical mass at a point where all players can engage together.
If you can't increase the numbers (and you won't), and two sides is off the table (which it is), then the only thing you can do is create much smaller maps with minimally spaced fields, and less fields total.