I really like being able to track individual ships in my games, but also appreciate having the option to track fleets for games that get a bit out of hand ship wise. If I had to choose one it would be individual ships with a ship cap per fleet.
One of the things I played around with in a starmada campaign system, was trying to tie things like supply to already existing rule mechanics in the game. Here's a snippet from one of my homebrew tests
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Supply:
Fleets need to stay supplied to remain combat effective. Once a ship leaves player controlled space, during the end phase, a supply roll will need to be made for every ship within a fleet. To do this, players will count the number of hexes to the closest piece of friendly territory. This will be the target number. Each ship will then roll aiming to meet or beat that number. So if a ship is 3 hexes away from a friendly hex, every ship in the fleet will need to roll 3 4 5 or 6. This effectively limits fleets to a range of 6 hexes from friendly space. Freighters may be used to modify these rolls, even extending the range beyond 6. However including freighters in a fleet takes coveted warship slots.
Cargo:
Cargo can be used to give bonuses to a fleet operating away from controlled space. This is done by granting a +1 bonus for every 100 cargo in a fleet. This bonus can be applied to any ship before the rolls for supply are made. The Federation Police Cutters cargo does not count for these purposes, and is not calculated as part of its cost.
Unsupplied:
One ships within a fleet fail a supply roll, they gain the unsupplied status. This will need to be notated on the fleet management sheet. Once unsupplied and ships strategic speed is halved (rnd down) & they only have access to half of their consumables (drones, marines, shuttles probes);rounded down. Further more, Tactical engine ratings are reduced by 1. This engine “damage” is not considered damage.
If a ship is unable to supply for a second turn in a row, additional effects take place. All consumables are considered unusable during scenarios, and each weapon gains the “non-piercing” along with another stacking -1 to engine rating.
If a third turn in a row takes place and supply still has failed, then each ship must roll a number of d6's
equal to it's current damage control rating, during the end phase that the roll was failed. A ship must make a 5 or 6 or be removed from play.
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I ended up not tracking individual ships in a fleet, and went to tracking supplies for the entire fleet.
Using much the same mechanic as transporters use in Klingon Armada, it made it easy for the players I had try it to remember the rule. I would love to see a supply system for fleets that kept it simple and easy to resolve. I found my system to work fairly well, but I know it has some serious limitations and would probably switch to something official in a heart beat.