Well, I try to raise:
- weapon skill (Small Guns for me) to 50 by level 10 or so (or melee, unarmed, big guns or energy weapons)
- science to 75 as soon as possible
- lockpick to 75 as soon as possible, but after science
- medicine to 50 or 55 by level 10 (for quests)
- sneak to 50 by level 10 or so
- explosives to 50 by level 10
- repair to 45 by level 12-13
- barter to 50 by level 15
- speech to 50 by level 15 (sooner if I'm a Charisma-focused build)
- I try to get both small guns and energy weapons to 60+ by level 18 for a particular perk
So I tend to tag Science, Lockpick and Medicine during the GOAT. Then focus on getting the other skills up quickly, without letting anything lag too far behind.