Technically, you could accelerate 'forever' but rocket science actually determine there's a 'topspeed' which is determined by the amount of fuel you have, its mass, and how burning that fuel grants you speed.
That's what I was trying to express in my inelgant way -- the real issue being how much fuel you have to decellerate.
Make entire fleets move at their combined averaged speed.
Alternatively, have the entire fleet move at 0.6 of the difference between the fastest and slowest ship. If the slowest ship moves at 7 speed-units, and the fastest moves at 20 speed units, then the entire fleet together moves at (7 + ((20 - 7) * 0.6)) = 15 speed units.
While I do think it's an elegant way to prevent fleets from moving very slowly, I don't think this would be very realistic (as far as space travel of this sort is currently realistic). The slowest ship can't move faster than its maximum speed, can it? Unless it has an overdrive of some sort, but then I'd apply some damage while this is active to show extra wear and tear.
Realism is enjoyable and definitely worth pursuing, but when it conflicts with enjoyable gameplay, sometimes it has to take a backseat. 
Weaker guns not doing much damage against a more powerful shield players can tolerate, but slow moving ships gets irritating really fast. 
The game can either just be silent about why the slow ships are now moving faster than normal, hoping most players don't notice (or if they do notice, they'll just ignore it and continue playing), or the game can create an in-game explanation for it.
Possible explanation: To move quickly through space, the ships warp space around them. The better they can warp space, the faster they go. The warped space is enough to cover the entire fleet. Therefore, either the entire fleet uses the fastest ship's space-warping drive (i.e. use speed of fastest ship), or perhaps it takes more energy to make warped space cover more ships, so the ships have to combine their space-warping-engines and you use either the average speed or a formula similar to what I had above.
Here's an alternative method of making old ships move faster: Use the same thrusters in every ship, regardless of ship level. But make speed be based on the fuel you provide your ships. As the player researches better fuel, every ship gets that fuel and can move faster.
But how does ships way out in space change their fuel? Answer: Magic. 
Or you can make 'fuel' part of the gameplay, so ships routinely have to return to your planets to refuel on a regular basis anyway, so they get the upgraded fuel the next time they return to port to gas up. (Note: Fuel doesn't have to be a liquid, it can be bronze, platinum, uranium, and so on, that you convert to pure energy to fly your Skylark spaceship using the 'X' substance you found while... </obscure sci-fi reference>).
[Edit:] Going off of Orymus3's post above mine, you can then have your spaceships have different storage capacities for fuel, to stay out in space longer. An entire fleet's storage gets averaged, because the ships can just transfer their fuel from one ship to another while in space (this should happen automatically without player micro-management).
If you have different speeds of ships and adjustable speed options what about having a lag behind option? You could intentionally make your invasion and anti planet ships slower then your main fleet so that they arrive a couple of turns later giving your main fleet a chance to clear the way before they arrive.
On the above post ideas. A common idea in sci fi is the hyperspace jump where ships have to exit hyperspace several times during a long journey to recharge the engines or refuel.
Your bigger ships might be able to open a hyper space window wide enough to encompass the smaller vessels. Flying as fleet might mean that a trip from A to B takes 2 jumps even though your rusted out old refinery ship would normally take 6 jumps to get there. In this way your ships don't so much have a "speed" but a maximum jump range per turn. Fuel ships could either extend the jump range or increases the number of jumps a ship can make before it needs to stop to refuel.
Realism is enjoyable and definitely worth pursuing, but when it conflicts with enjoyable gameplay, sometimes it has to take a backseat.
Weaker guns not doing much damage against a more powerful shield players can tolerate, but slow moving ships gets irritating really fast.
Fun is indeed more important than realism. I guess I missed the part where Acharis wants to remove micro management, which my suggestion would more or less require :)
Many observations made so far point in the same direction: speed differences make little sense and can be eliminated as a source of pointless annoyance.
If FTL speed differences (like in Star Trek) are needed, they can be simplified to a few tiers and used to forbid ships with different speeds to belong to the same fleet. Serious speed differences are going to imply different strategic movements in any case.
If limiting thrust of realistic engines according to available fuel is a normal occurrence, it can be assumed that the fleet automatically allocates available fuel to maintain the same travel time for every ship, rather than slowing down specific fuel-challenged ships. Computations are easy: fuel is proportional to ship mass.
In principle, I would rather remove than add :) Especially if it's something as minor as fleet speed.
Adds an economic layer to fleet management!
It has a game design appeal for sure... But those annoying players, they will scream it's unrealistic :D
Make entire fleets move at their combined averaged speed.
Yes... Still, it's so cute to have those slow big ships :D I don't know, it's both annoying and fun at the same time to me :)
Many observations made so far point in the same direction: speed differences make little sense and can be eliminated as a source of pointless annoyance.
Still, it's so cute to have those slow big ships
I don't know, it's both annoying and fun at the same time to me
I can see the benefit of slow and powerful ships. I can see myself tolerating that (just barely) as long as they aren't too slow. But outdated (i.e. weak) ships that are also slow are an annoyance.
