Honestly, I don't think that large scale battles will happen very often. The problem is resource balance. If ships are cheap to build, resources won't be valuable and there will be no reason to fight in the first place. If ships are expensive, people won't want to risk their hard earned equipment. Based on how complex construction in Starbase is, I assume we're headed towards the latter scenario. Battles will likely come down to who brings more ships, with the smaller side surrendering and either joining the larger faction or fleeing to avoid their ships being destroyed. Large scale battle will only occur when both sides are equally matched, which will be rare. Factions won't be inclined to pick fights with others of the same size because even if they win, their fleet will still take losses.
Of course, the PVP meta will also play into this. If small fighters continue to dominate, it may be a blessing in disguise. The smaller the craft, the lower of the cost, which leads to people not caring about losses as much. Additionally, pilot skill is more relevant in dogfights, such that an outnumbered force could possibly even the odds if they are experienced pilots.
Another possibility is that everyone will simply be friendly with each other. Depending on what bonuses are gained from owning territory, it may simply be more profitable to trade with your neighbors as opposed to taking their resources by force. If a mega-alliance is formed, they could easily weigh their collective might against any smaller warmongering faction and put a stop to major conflicts altogether out of fear.