Well if you know exactly where you want to spend those points prior to running the game. You can just set up an actor effect that is checked "PC start" with the geck.
To do that ... In the object tree ... go to "Game Effects > Actor Effects > Ability " then right click in the list and select new (right column of object window)
A window will pop up named "Actor Effect" ... Give it an ID , example "00SpecialBoost01" The 00 is so it will show at the top of the list , and the 01 is incase you want to make a few other boost senario's. But remember you only want to have one of them checked as "PC Start Effect" for this simple fix senario.
You can name it if you want , but the ID is usually good enough. Then make sure the drop down says "Actor Effect" And check the PC start box.
Now right click in the large field to the right and select new. Another window will open called "Effect Item"
At the top left is a drop down box where you select the effect to add ... you'll be looking for stuff that starts with "Increase"
Just browse through the list which is alphabetical ... so "Increase Agility" will be above the rest of the others , wich are mixed in with other stat increases.
So select a stat ... make sure it says "Self" from the drop down , then just click in the magnitude , and type the increase you want ... example 1,2,3 etc...
Then click OK ,that window will close , and you will see that effect added. Now right click in the field again and select new repeating for every special stat you want to boost. If you want to change one ... just double click it to open its "Effect Item" window
When your done , just click Ok on the Actor Effect window ... Then go to "File" top left header and save it as an .esp ... that you will then put in your load order. That's for making a separate file by just loading the Fallout3.esm
But you can load up another .esp making it the active file , and just add that Actor effect to it (make a back up of it before though)
Hope thats clear as mud for ya ... hehe ... But seriously ... just ask if something is not clear.
Add edit: Just wanted to add ... try that out ... but later if you want , can explain how to set up some activators for the room with the special book ... which you can pick for different special boost mixes. But then again , You can maybe add special points to the pool they give you ... just not sure how yet. Or if its even possible without editing XML which is beyond my expertise.