One issue I have noticed is that fleet combat isn't that decisive because if one side is outnumbered they can easily warp off, even with the tower that slows the speed of hostile warps it doesn't give you enough time to kill much more than a few ships.
One idea I had to counter act this was to add cap ship that has the ability to prevent ships within a certain radius from warping off. I think something like this would be best suited for a cap ship with low offense and fairly strong defense, some of the other ability's it could have would be along the lines of fleet support, maybe couple of passive fleet boosters such as shield recharge, targeting. Or it could even be a hostile fleet debuffer such as reduced range, speed, (these two would be good considering the primary ability of the ship) or reduced damage, shield recharge. Considering the power of the primary ability of the ship while active all weapons should probably be disabled, this way if you want to use the ability you have one cap ship less for dps.
As for the range of the warp disabler if it is a ability that can run forever with a toggle switch it shouldn't be too large and/or the ship should also no longer have the ability to move while the ability is active, or at least at a significantly reduced speed. If the ability is only able active for a certain amount of time and requires antimatter to activate then the radius should be fairly large.
My ideal ship would have these ability's:
1. Warp Disabler (effects all ships in range) - lasts for 30 seconds (doubled each level), large radius, while active all weapons and ships engines are disabled.
2. Reduced Velocity & agility (effects hostile ships in range) - lasts for 30 seconds (doubled each level), slightly smaller range than warp disabler, level 1 is 10%, each level after adds 5%
3. Passive Shield Boost - passive ability which improves the shields of all friendly ships in range
4. Overheat engines - provides a quick burst of speed to help get into range of a hostile fleet at the expense of some damage.
As for antimatter costs using 1 & 2 should require all the ships antimatter maybe 200 antimatter and 100 antimatter, and 4 costing 50. This way you couldn't burn on top of the fleet stop them from warping and slow them down.
These are just rough ideas, feel free to add any other suggestions or why you think this is a terrible/great idea.