How best to handle skills in Mothership and in other OSR systems is a recurring discussion. Folks have addressed this in the context of level-less play, debt for skills, tweaks to the details of the skill table, etc. Mostly, those approaches have been satisfactory when I've used them at my table. I've noticed a few issues, however.
Some skills are keyed into concrete mechanical benefits and in campaign play are borderline mandatory. Others are essential to certain character backgrounds but don't necessarily come up that often (zero-g is the worst offender), knowledge type skills can slow down investigations and some, like mathematics or hyperspace may only come up once or twice in a campaign, and finally the scientist skills don't always fit together logically and, without house rules, don't adequately reflect a skilled professional. The most obvious example is that in default MoSh a character playing a doctor will never get the surgery skill at the start of the game. Many of these issues can be (and no doubt will be) addressed in the boxed set without making any radical changes to the skill system.
The approach I propose is a bit more radical and a lot more minimalistic. First, it relies on the fairly orthodox OSR assumption that most in-game problem solving shouldn't depend on what you have on your character sheet. MoSh actually does a pretty good job at this insofar as the skill list mostly capture things outside of the realm of player common sense but I'm going even further. Players coming from DnD or other games with very concrete skill lists will probably have a harder time.
The core assumption is simple: your character has knowledge and skills consistent with their class and background. When your character's background would justifiably give them a substantial advantage, they make an appropriate ability check with advantage. Sometimes having applicable background is a prerequisite to rolling in the first place: in that case, they don't roll with advantage.
In practice, there's a little more to it than that:
- The benefit of rolling with advantage is larger than a regular skill bonus (about +20%); accordingly, skills should be narrower. Someone with a doctorate degree in xenobiology will be screwed when they're up against plants or viruses.
- When your character's background would give them relevant knowledge about something, just tell them what they know without rolling. I do this even when using the regular MoSh skill system and it makes the scientists feel a lot better about themselves.
- Marines start with proficiency in automatic weapons. Characters who roll a relevant background also have proficiency in automatic weapons. Everyone else gains proficiency by surviving an adventure in which they used an automatic weapon and taking an appropriate amount of time to train. If you're playing a campaign where you don't expect characters to take firearms skills you can make things a little more difficult by requiring more survived missions or requiring a character to pass a fear save in addition to spending their downtime training.
- Nobody gets the skill bonuses to attack. Tough shit. At my own table, there are better weapons, cybernetics, and Meat solutions to shooting better; these provide between +5% and +20%. If you don't provide these options, you might find that certain high INSTINCT enemies are tougher. I don't view that as a bad thing.