One of the things that I'd like to do to help characters distinguish themselves is add the ability for each character to purchase a Background and an Affinity. These are separate from Background skills - each allows a character to have something that they can spend LP (again, assuming Ares) on to give them a special effect or a critical success on certain rolls.
The purpose of this is two-fold: one, to slow down character growth by giving people useful things to do with their LP outside of just buying stats and skills, and to allow character past the XP cap for stats and skills to continue to spend LP on things that aren't just background skills.
Example of a Background:
Criminal: You’re no stranger to the underworld and the skills required to survive there, whether it was a bit of smuggling on the side, or full-time wetwork for one of the many criminal organizations of known space. You can spend an LP to auto-succeed on an uncontested (by PCs) Stealth roll, and gain the Background Skill Cracking Security: ** for free.
Example of an Affinity:
Technowizardry: You’re one of those people who probably ended up in tech support (formally or not) and whenever you walk in the room, whatever was going wrong works again...until you leave. You can spend 1 LP to make a piece of broken technology work again. This technology is not fixed, but it will do what it needs to do just long enough for you to finish an immediate task. For multi-system technologies (like the Excelsior), this effect is limited to a single console or subsystem. You don't have to know what the technology is SUPPOSED to do, but operating something without determining its function first is a good way to get vaporized.
So, as you can see - Backgrounds give you the ability to spend LP to really nail a single roll when it counts, as well as a free Background Skill. Affinities offer a way to spend an LP to create a more qualitative effect. Both are meant to provide an LP sink, but also to give people ways to create characters are more than their stats and skills, without having to create five hundred 'special abilities'.
Further customization, though, can be found through genetic and cybernetic enhancements. These won't be widely available at the start of the game (since the crashed ship doesn't have a fully functioning genetic manipulation bay, or cybernetic surgery), but both of those things can be established through the Project system.