Oh this is good question. So this my idea how to make pvp more funny and also how to put more importance onto guild function and guidies responsibilities. I really enjoyed such similar PVP system in MMO I played before SWTOR. Idea is to combine PVE and PVP content of this game.
Each guild can get or buy small base camp. Camp can be also point where you can meet other guildies and you can profit also from rested state like in cantina.
For example, base camp can cost 20kk credits and you can buy it immediately. You get automatically mail droid, med droid, GTN, travel portal to dailies areas and etc.
Or you need to wait two months after guild registration to get it free. Anyway meantime, you should manage your guildies to save certain money in guild bank. When you get camp, it will be empty and you must buy all needed and required items. This should be finally little bit cheaper than option 1.
When you have camp, PVE content start. Using credits, different material, etc you must upgrade your camp to small fortress. Building, protection walls, shield generator, defensive turrets, etc. Every member of guild can help with this. In this PVE content, there should be some limits for camp upgrade, but some of latest upgrades will be so difficult and expensive, that it will really require high focus from all. As there are a lot small guilds, guild which own camp can sign off partnership contract with other guilds and for example 3 small guilds can have one camp.
Lets talk about PVP content now. When your fortress is ready for war (required minimum upgrade), you just register for guild fight (1 guild against 1 guild). There should be regular events of it, f.e. twice per week. Registration will be done one day before war. There should be also some guild rating system to prevent that guild begineer will meet experts in war. Such fight will be very annoying. Fight itself can take max 60 minutes. During this time, both guilds must have strategy to improve your fortress, to properly defend it, how and where to attack, etc. Fight will finish after 60 minutes or when one guild destroy enemy fortress (f.e. takeover of headquater).
There must be several other points in this war, like attacking and defending certain objectives. Number of kills, number of captured and controlled objectives, or some other progress rating will be key factor for fight result. Winner will get point for his overall rating, second guild will lost points. this will be important for next war registration.
Something like this is generally what I wish to see in SWTOR sometime in future. Current pvp content is very boring for me, and I do it practically only to get some pvp gear items like relics.