In regard to what can be changed, I'd like to agree with the s2tg_bowl's suggestion about pvp. It would be more efficient to place the pvp marker at the end of the Antares system story missions, and have this act like the beginner missions where players whom have reached a certain level of progress in the story missions cannot aid new players. This will increase the level of teamwork between new players in the first two systems, and will promote the creation of more clans. The more variety in clan choosing, the more appetizing the overal game will be. Add on a pvp safety for antares and vega systems and not only will you be promoting the building of Pirate Galaxy's in game community, but you will also be allowing new players to gain more experience in piloting their ships and collecting the neccesary blueprints/cryonite they will need without worry of higher ranking players (whom at times farm for rare blueprints in these systems) shooting them down accidentaly. A sol ship makes quick work of antares and vega ships, and the ability for these players to shoot at those who aren't capable of aquiring stronger ships is not neccisary.
Instead of Game Sages, another option would be to instal some kind of bot to public chat that can regulate the public chat posts and filter bad language automatically. Aeria's other games have this, and it seems to work tremendously.
If the prices of items such as rare blueprints, high level ships, armor upgrades, conquest levys ect. stay so high, maybe double, or even triple the base cryonite drops in systems where a lot of cryonite is required to build these expensive ships. Going from technatoria, where your basic drop is around 45, to baumar where basic drop is 50 is far too little of an increase when mizar ships cost more than double the price of gemini ships. And lets face it. even 40% bonuses from conquest planet ownership is barely visible when you're dealing in 30-45 cryonite. In sol system, your basic drop is around 63-70 cryonite, but it costs on average 100 energy to use the weapons that are available in the system. To add on to this, the armor of sol mantis and imp ships is so high that it costs 1000-5000 energy just to destroy a single ship, then the drop rate for cryonite is around 25%, yet the cost of a lvl 40 ship is 11,000 cryonite, and to fully outfit and armor one would cost another 22,000. This adds up to more than 200,000 energy needed to fully armor and equip a level 40 ship. The elite membership cap for a lvl 40 player is around 38,000 energy, and the non member players have around 8000-10,000. So if you play nonstop 24 hours a day for 7 days a week, you might be able to build a sol ship if you don't have elite membership (the highest membership available). The result of this is that players are more likely to get frustrated and move on to another game.
As far as conquest planet bonuses go, in order for this to be an effective bonus they have to be set over 50% per planet to create an incentive to participate in conquests. Another option would be to award AP at the end of the week to the members of the rank 1 and 2 clans on the ladder for both warscore and conquests won. This will inspire more competition and promote more player activity.
I also agree with the three color scheme for ships. That would be rad.