1) Character creation determines initially available hullmods. For example, a bounty hunter would know auxiliary thrusters and safety overrides, a scavenger reinforced bulkheads and insulated engines. Of course all the other hullmods can still be discovered.
Advantage: More variety in early loadout design, more (lore and gameplay) distinction resulting from character choice.
2) Character XP gain increases with deploying fewer ships, within a range. The maximum XP can already be gained by a relatively small, but not too small task force that should still reasonably stand a chance against the enemy without the use of exploits or cheesy tactics.
Advantage: encourages restrained deployment, and thus interesting fights, against same-sized and inferior fleets. At the moment that is encouraged only by deployment costs, which is counteracted by the increased chance of losing ships.
3) Smaller fleets can get some loot from bigger fleets in an escape scenario, if they manage do destroy ships. Doesn't it feel unfair if you are caught by an overwhelming enemy and fight some heroic rear-guard action where you destroy a third of their ships, only to be left with empty hands? It doesn't even make a difference if you manage to destroy most of the enemy or none at all.
Advantage: Encourages small-fleet playstile und reduces reloading-if-caught-syndrome.