Personally, I was a fan of Fallout's (1 & 2 mainly) Perks system. Every 3 (or 4) char levels, you get to choose from a(n all-inclusive) list of Perks your character is eligible for. Skill Points were distributed however you wanted. Fallout 2 let you max-out your char (almost) completely at endgame if you wanted as well (you couldn't max out base char stats.) This was just a reward for finsihing the game though. Still, at level 99, you had 33 Perks and maxed (300%? Or was it still 200% in FO2?) skills.
I found Fallout's skill system to be both fairly straight forward and flexible in character building. I liked it a bit more than usage-based systems, like The Elder Scrolls' various systems. Those reward you for constantly using a skill, but gameplay-wise, they aren't very balance is opportunities to use the skills you wanted to raise at times. (Like RUNNING vs SNEAK vs SWIMMING). I found the usage-based skill system to be rewarding in a sense, but not very flexible in the mid to late games (early game doesn't matter too much since all your skills are essentially at crappy levels.) Once you peak out certain skills by mid game, you're kinda locked into a particular play style unless you grind to build up the other skills. (Part of the reason I despise MMORPG: they lock you into specialties and by my very nature, I like being a jack-of-all-trades to some degree with slightly higher competency in a few things. I might not be the best or an expert, but I can still hold my own in any situation.)
I also never really liked skill-tree systems eithers. They give you "choice", but once you make that "choice", you tend to be stuck on that path with little or no recourse to backtrack if need be. I understand it's a valid gameplay mechanic (consequence of action/choices), but I never really enjoyed having to play a game start-finish just to TRY OUT a particular char build to see if I like it out not. (Especially games with class-based skill systems for the player character.)
A lot of Alex's choices for gameplay mechanics seem to be rooted in simplification and abstraction of complex mechanics (KISS - Keep It Simple, Stupid). I think something akin to Fallout's Perk system would fit well with Satrfarer. Especially since it seems like the "skills" in SF all look to be "always on" passive bonuses (this was the case of the Perks in FO, if I recall). Active skills seem to be wholly based on the ships themselves (i.e. ship systems.)