Some folks really, really, really are bothered by the number of skills available. This attitude has always surprised me, though I don't question its validity for those concerned, so let's explore thinning out skills in the StarCluster system.
One thing you should always keep in mind - reducing the number of available skills directly reduces character options and thus character flavor. This is an asset in some genres, like Pulp, with its strongly drawn archetypes, and supers, to whom skill use is of minor importance next to Powers. It is not an asset in genres with subtle differences between character types, but if you are bothered by number of skills, this is presumably not a problem, or is taken care of in other ways.
Reducing the number of skills itself is not a problem in the StarCluster System. Since all skills are center-defined, as a skill is removed, the other skills close by naturally expand to take up the slack. For example, medical skills in standard StarCluster 3 would be Diagnosis, Treatment, Surgery, Drug, and Herbalism. If you removed Drug, Herbalism, and Diagnosis, you are left with Treatment and Surgery. Just subsume some of the damage that would be healed by Drugs or Herbalism into the other two skills' healing, and you are set. You could also roll Treatment and Surgery together as well, if you want to, into a Medicine skill, also increasing the damage healed once again. Using this collapsing process, you can bring the StarCluster galaxy of skills down to about 20 core skills, or anything in between, as Klaxon did for his supers game, Look! Up In The Sky!.
Now you need to change the rate of skill acquisition by the compression factor - the ratio between the starting number of skills and the number you ended up with - otherwise you will end up with supers in every hovel, and everyone able to do everything at a Master's level. For example, SC 3 has about 100 skills, including PSI skills. Compressing it to 20 skills gives a ratio of 5 to 1, as 100 divided by 20is 5. If it takes 5 years to learn 5 skill ranks in standard SC3 professions, then it should take you five years to learn 1 skill rank in the compressed Skill version of professions. This ratio would also give you 3 Background Skills for your first 18 years. As for education, an Associates degree would give you one skill in 2 years, a Bachelors 3 skills in 4 years, a Masters 1 skill in 2 years, and a PhD 2 skills in 4 years.
You would probably have to mess around with the professions of course, but that would be relatively straight forward, and would need doing if you were customizing for a setting anyway. Doing this will give you a game that will play just fine by SC rules, using any of the resolution mechanics, with the number of skills you want.