Currently, there's a lot of skill upgrades that may not apply to you, which you need to take to get to another, unrelated skill (like having to take derlict contingent to get to a second colony skill). So here's a way to change things around.
Instead of one experience track, you have a few, and the experience you get is sorted into categories: exploration, combat, command, and governance. Get each of these doing relevant things, and you can choose skills based on those categories.
Exploration:
Gain Exp- Finding new systems, finding things in those systems, salvaging fancy items, surveying planets, etc
Skills- Covers salvage, efficient travel, burn speed, sensors, surveying, etc
Combat:
Gain Exp- Destroying enemy ships with your ship, surviving battles without losing your ship, etc
Skills- Combat skills for your personal ship
Command:
Gain Exp- Giving orders in combat, having your other ships defeat enemies, surviving battles without losing ships, etc
Skills- Officer improvements, fleetwide combat skills
Governance:
Gain Exp- Founding colonies, hiring administrators, surveying valuable planets, building industries, arranging trade deals
Skills- Anything to improve colonies
This also allows for more granularity, as you've got four skill trees to play with instead of just one. You no longer have a character level, you just have a level in each tree. You can now have things like skills that just boost one industry, or even part of one industry (like +1 mining, or +1 mining organics) without that being too much of an issue (and that also means you can have far more specific administrators that are ideal for certain planets but not others). You don't have to choose between "my ship is cool" and "my fleet does well", it's just a question of how you focus your playstyle.