So I was wanting to make the game a little harder by making the character start out at 1 or even 0 skill level at all skills. I am hoping this would have two effects, make the character be able to level up higher in the long run, and be able to get more perks by leveling more, making the game harder at the start but the character more powerful at the end, for hopefully a more gratifying experience.

Unfortunately I'm lost in the new creation kit, and papyrus seems like a mess to me, where I could script anything I wanted in Oblivion. Writing a script to setAV for all the skills would be easy, but I'm going to wait for some tutorials aimed at humans before I get involved with Papyrus.

I found the player actor named prisoner and I'm assuming this is the default character. I tried to edit the values of the skills but it wouldn't let me lower them. I could raise them but not lower them. I can add a positive number to the "offset" and raise it, but I cannot use a negative number to lower it. Any idea how to do this?

Just poked around under Settings, and found the following item that may be what you're looking for:

iAVDSkillStart 15

which is the default starting level for all skills. Racial bonuses are applied on top of this; I first tried editing those, but they only allow positive numbers as well and there are a max of seven of them for each race (you can edit which skills get the bonuses, though). As you are looking for a harder start there are two more values you may be interested in:

iAVDhmsLevelUp 10iAVDSkillsLevelUp 8

which control how much you get to increase one of the three attributes per level as well as the base number of skill gains needed to reach the next level. Note that the second value has a scalar applied to it, which causes it to increase with each level gained; if I can find said scalar I'll add it to this post (I suspect it's hard-coded, though), as manipulation of same would allow for adjustment of how long it takes to gain a level.