I have no idea what you have planned for the end-game right now, if there'll even be a PvE option. That said, I heard on hailing frequency that you had to make a design choice between making a simulator and making a game and I think you should stay true to that.
Right now, a lot of the fleet battles are about killing 50 ship X to progress to the next phase which is usually something similar, kill 50 more ships/do some scanning while fighting some ships anyway. Thats fine for low levels where you can't expect a pug to have much coordination, but I hope you have some Aces planned for the level-cap encounters. Encounters where you need a plan to win, and even with that plan, there's still a chance you will fail... yes, that's right! I'm suggesting you make SPACE RAIDS!!!!!
Rather than blabber on about what I like about other games, I'll make my suggestion by roughing up a design for a PvE end-game encounter.
The Epic Battle of Pinata Station
Pinata station is a huuuuge space station in some place really important, the players must destroy it get to the sweet sweet candy inside.
Phase 1 - Trash fights
The players begin by mopping up some basic defenses in the outer perimiter of the station. Theres a few ships, a few orbital weapon platforms and some fighter squadrons. While the space station will not attack the players while they fight these skirmishes, they are close enough to the main station that should the players attack the station before destroying them, they will notice and move in to attack. If the players choose not to clear these trash fights, they have essentially failed already.
Upon defeating the last trash pack the station sends out a distress signal for reinforcements. The fleet now has 25 minutes to defeat the station.
Phase 2 - Disable the defenses
The station is somewhat similar in to DS9 though much larger. There are 5 outer blades, each protected by a their own individual shield. The fleet must burn through this shield to take out some turrets. The turrets will fire upon the fleet as they attempt to break through the shields doing moderate but easily "healable" damage.
Once the shields on a blade are down, the stations repair crews will attempt to restore power to them. Part of the fleet (5 players) must beam down to the vulnerable station blade and proceed to eject the power core that is located inside it. This is a relatively simple fight for the ground team, the main emphasis of these away missions is that they only have around 15 minutes to eject all the cores (3 minutes per blade). To eject the core the players must defeat an enemy team and use the security dongle off a dead engineer to access a computer console.
To stop the players from being able to attack multiple blades at a time shortly after an away team goes down, a small squad of nearby ships will arrive (1 ship for each player that beams down). Knowing the greatness of Pinata stations candy, they will do anything to protect it for the good of the empire and each set themselves on a collision course with a captainless ship. The remainder of the fleet must burn down these behemoths (will take the best part of the 3 minutes the away team has) before they collide. Since it's a race against the clock, losing a ship here will decrease the fleets chance of candy.
While the players fight to eject the cores and help the defenseless ships, Pinata station has another trick up its sleeve in the form of huge torpedo batteries that spell insta death for any ship hit by them. The players were aware of this though and their fleets intelligence planned their attack for when the station was putting their targetting systems through maintenance. While the engineers of Pinata station were skilled enough to get them operational, they are working far from optimally. Every minute or so, the station will attempt to lock on to 4 randomly chosen captains. The captains will be aware of this because of some funky spell effect that stands out during a battle. These captains must fly behind the asteroids/hunks of metal that the trash guns were placed on and use them as cover. Due to the massive damage these torpedo batteries do, they will destroy the cover the captain has hidden behind. If the players take the full 15 minutes to complete this phase then when all the cores have been ejected, there will be no cover left.
Phase 3 - You no take candy!
Things are looking grim for Pinata station, but if you're gunna get smashed open for your tasty candy innards then you may as well take as many of your attackers as you can with you.
By now, the fleet now has 10 minutes to destroy the station before reinforcements arrive. With all the cores ejected the main body of the station has loses its shields shields. The 4 torpedo batteries continue to fire approximately every minute but by now there is likely no cover left. Each battery will take approximately 1 minute to destroy meaning the fleet *will* take substantial losses here (4 after 1 min, 3 after 2 min... 10 total). Once the batteries are down, it's essentially just a dps race to destroy the hull before the reinforcements arrive.
If executed without casualities (excluding the phase 3 torpedo kills), the players should find they have 1-2 minutes left on the clock. However, the fight is long and the dangers of Pinata station are many so it will take a fleet number of attempts to succeed, let alone perfect it!