One thing I have noticed around here is that people don't totally understand how things move in space. So I will put out a few things that I know of about space (if any of these are wrong please let me know).

Size: Depending on the mass of the ship and the power output of the engines you can technically make your ship however large you want. For example you can have a ship a thousand miles in diameter that is simply a large empty balloon, and as long as the mass of the ship is low, you only need a small amount of power to move that large ship. However, if you take that large ship and now fill it with concrete so you have a thousand mile ball of concrete, and use the engine from the balloon ship (assuming that it was just powerful enough to get the balloon ship accelerating fast enough to cause anything inside the ship to be under 1 Gravity of acceleration), then your concrete sphere will NOT be moving at 1 G acceleration because it's mass is larger. There is no friction to prevent it moving, but in order to get this large mass moving you need a larger output of power. This is not to say the concrete sphere will not move, it is just that it will not be accelerating at the same speed as the balloon ship.

Friction: In space there actually IS some friction, this comes from mainly from cosmic dust, solar winds, and various small bits of space debris, and to a lesser extent the energy that is radiating off of the ship itself. Space is for the most part not actually empty, there is somewhere around 5 hydrogen atoms or so per square meter (this is usually higher or lower depending on distance to nearby stars). So while 5 hydrogen atoms per square meter wont slow your ship down much, if you move through space fast enough and long enough, then there will be a noticeable effect. However in the distances involved in this game (and as long as engines are on) then there is essentially no effect of friction on the ships.

Acceleration: In space the generally most useful form of describing how good a ship is for speed is in the ships ability to accelerate getting it closer to the speed of light (or beyond as it may apply). All ships depending on the engine/fuel type have the ability to almost reach light speed (in physics it is impossible for anything to actually GO lightspeed). However some engines can get you there faster. For this I like to use the Honor Harrington system to explain things. All the ships in the HH universe have essentially the ability to accelerate their ships to massive speeds very quickly, however if you accelerate too fast then you turn your crew into a very thin goo and also risk ripping your ship apart. So to counter this so you can accelerate fast they have a system that cancels the effect the accel has on the ship to a limit. In the HH universe the way for ships to go faster is not to get bigger or better engines, but to get better systems to deal with the forces of accelerating faster so you can reach the speed you want to go FASTER then the other ships can.

Speed/Inertia: Speed in space is about half the battle. The faster your ship closes on the enemy ship the shorter your battle will be because you have to slow down, turn around and then reengage. The reason for this is inertia. Think about running the 100 meter dash. If you are running full speed and then try to stop moving exactly at the finish line (by stopping running), then you are going to be thrown forward by your own inertia and sent sprawling to the ground. This is because when you are moving at any speed, to reach zero miles per hour, you must first slow down, you cannot go from say 20 MPH to 0 MPH in exactly zero seconds. This is the same for ships, except since they have no ground to trip on and fall down and thereby stop, they will keep going even after their engines are turned off. So for a ship to stop, you have to turn it over and turn the engines on again (essentially accelerating the opposite way) and because of the limitations imposed by how fast you can accelerate (assuming you are slowing yourself down at the same rate) it will take you the same time slowing down from a speed as it took you to speed up to that speed.

Mass: Mass is essentially the amount of matter that is in a given object. The more matter a ship has the more mass it has. In order to get a given amount of mass to move at a given speed, you have to use a certain amount of energy, think Mass + Speed = Energy (note that this is an oversimplified equation used to help explain the concept). However if you increase the amount of mass or speed in that equation, then the amount of energy need to get that mass to that speed is larger. So to get a scout ship moving at 100 miles per second you will need less energy then you would need to get a battleship to 100 miles per second. If the engines for both ships are the same then the scout will get to that speed faster then the battleship. However if the battleship has a better engine (by better I mean more efficient in terms of output energy to mass of ship and to a very small extent the size of the engine) then it can possibly be "faster" then the scout. In terms of comparing if a ship is faster then another ship you don't use speed, you use rate of acceleration. Example if a ship has an acceleration of 100 G's and another ship has only 50 G's of acceleration, then the first ship is "faster" then the other ship.

Engines/Fuel: I have lumped these two things together because they go hand in hand. For engines the faster engine is the one that can accelerate a given mass faster then another engine. For an engine to be better at accelerating that mass, it has to output more power in a given unit of time then another engine. This is where fuel comes into the equation. Depending on the engine type different fuels will give different output powers. For example, in a combustion engine gasoline has a higher output power then alcohol (I believe), because when gasoline burns it releases more energy then alcohol does when alcohol burns. Therefore an engine based on gasoline will be able to move faster then one with alcohol. Now for chemical engines like the shuttle this is the same thing. If you have a rocket based on chemical A and another on chemical B and B releases more energy then it will move faster.

Well this post has been a mouthful, but the main reason I started it was to explain as much as possible why it is that a scout with it's smaller engine will move faster then a battleship with it's larger engine. So assuming that all ships in a given sides fleet use the same type of engine, then ships with smaller engines will be able to accelerate faster then the larger ships because of their low mass, the larger ships have engines that are larger just so the ship can move at all in the first place. This is also partially why missiles will move faster then any other ship.