So it turns out that I like some of the agility abilities, but I'm about 4 hours into the game, I only set my agility to 2 in the beginning does this mean I can only choose the first 2 perks in agility? If so is there anything I can do to change this

You can use your perk points to increase your agility

So what was the point of picking things in the beginning? What do I get for picking higher levels on things in the beginning

Access to higher level perks...

oooo so basically it allows you to pick and choose higher perks for things instead of having to go in order?

It's not locked in that way. You have access to whatever perk you want so long as you meet the requirements. You don't have to have the first perk in agility to get the second one

Well I just tried to rank up sneak, which is the 3rd one down on the agility list and it won't let me rank it up, how do I get to rank that up??

You will need a SPECIAL of 3 in Agility.

Increase your SPECIAL at level up instead of buying a perk.

Yeah just figured that out right after I asked sorry for being [censored] for a second thanks for the quick responses