[quote=@MissingAxis]
[@Willy Vereb] As long as your mechs aren't going to be mowing through battleships as easily as several of them just did in that video, I don't really care if they use energy weapons or ballistics. 
[/quote]It really depends on tactics and how a ship is equipped to fight enemy smallcraft.
Without shields it's really about who can better damage the other. A smallcraft is less armored and there are more kinds of weapons to bring the hurt with but so there are weapons you can equip a fighter with which can take down the ship.

It's a bit weird but think of the relation between naval warships and fighter planes in WW2 with a twist.