Someone mentioned there wasn't any problem cramming all the skills into one giant tree, the main problem was you couldn't scroll the display. Simply resizing the graphics and editing the .ini files should work although you'd have to scale it for all pilots.

Ditto the active perk icons above each pilot's icons; they supposedly stack higher and higher until you have so many they're rendered out of sight. Resizing the icons and finding out where the size is defined may fix this. Fortunately passive perks aren't displayed, but on the flip side we can't choose to toggle passive perks on/off. E.g. if you have a bunch of perks with bonuses and penalties you might want to have only several in use at a time - unless you want the player to permanently live with all the bonus/penalties.