Sure, the Flagship doesn't have to be the biggest and meanest, but, it would be a ship that stands out, that give personality to the whole fight. Since it would be a personal pet of the players, it would make sense for it to be a bit tougher so that you can care for it properly and retreat it if things look bad.
As it stands now, the game doesn't have any personality. You build a myriad of ships and send them off to fight. There's never an incentive to zoom in to see your ships in action.
A Flagship could take this role, it doesn't ave to be the most offensive of ships, but it should have good defensive capabilities. You should also be able to customize it to a certain degree. It should give, as mentioned above, bonuses to nearby ships, a great idea.
Yes, that's what I meant when I outlined my second idea about seperate and unique flagships. I never meant to say that these ships have to be super powerful. I did, however, mean that they are unique and have special abilities that make things a little more interesting. Also, you're allowed all three at once, but you can only have them out once, so if you lose one of the three, it's gone.
One of those three ships would be your Fleet's flagship and thus all ships would gain specific bonuses depending on which you designate.
Here's an example on how I meant the actual Flagships to be like:
Flagship One: Rear Admiral Hashimoto's Blazer
The Blazer is a suped up frigate that grants all nearby frigates a small increase to Speed and a reduced chance of being hit. Furthermore, the special ability of this ship is to allow all frigates to ignore the effect of Jump Inhibitors as well as giving out a reduced jump charge time. So, you could use this ship for small, fast raids into enemy territory to mix things up so your main fleet can rush in. Obviously, since you only have frigates with you, you wont be able to defeat a whole fleet with capitals but you will be able to harass trade, research and resource gathering.
Bonuses for using this as primary "Flagship"
1. Due to expert knowledge in fleet maneuvers, slightly higher speed and maneuverability for all ships in the vicinity.
+ Speed
+ Maneuverability
+ Fighter and Bomber Speeds
Why choose him for primary "Flagship"? Quicker Response times of fleets as well as mobility in countering enemy.
Flagship Two: Admiral Vestov's Commander
The Commander is a cruiser sized vessel designed to act as a C&C ship, giving Cruisers in the vicinity a lower antimatter requirement for special abilities with a decreased Cruiser special ability cooldown. Ultimate support for our cruisers on its own.
Bonuses for being Primary Flag:
2. Due to strict drill routines and maintenance, Vestov increases shield and hull regeneration rates and decreases build time for defense structures in orbit.
Flagship Three: Fleet Admiral Fenrik's Crusader
The Crusader affects Capital ships, giving them increased Hull HP and faster rate of fire to their weapons. This also extends to fighters/bombers so the Carrier isn't left out. He's designed to augment the survivability of capitals.
Bonuses for being Primary Flag:
3. Fenrik's determination grants all ships higher armour. Planets have an increased resistance to bombing and recouperate faster. Shipyards construct ships quicker.
Each ship would have a unique look and (hopefully) the voice-over for each of the Admirals would be unique to add some extra personality.
I just made this up on the spot to give you guys an idea. Instead of these passive abilities, similar ones can be placed as regular anti-matter skills.
There are a lot of possibilities, this is what I suggest.