A few things...
With Comprehension, there's about 25 skill books for each skill and each will give 2 points. That's about 50 points per skill, roughly speaking. Then there's a bubblehead for each skill, which gives 10 points. That means 60 free points per skill, by and large.
Now, if you start with 9 int (and there's no pressing reason not to) then you'll get 19 skill points per level. Once you get to the Int bubblehead, it's 20 skill points per level. Whether you get that bubblehead at level 2 or at level 5 is really insignificant. It's just a matter of 3-4 skill points, which you won't miss in the greater picture. And no, you can't avoid getting to level 2. It happens when you leave the vault, regardless of difficulty.
Anyways, back to the skill point math. As mentioned above, you can by and large get 60 skill points for free, for each skill. If you get Almost Perfect and then add the SPECIAL bubbleheads afterwards, you'll have 10 in all attributes, which puts all your skills at 25. 20 from non-luck attributes and then +0.5 to each skill for each point of luck. Thus you really only have to get the 13 skills from 25 to 40 to max all your skills. That's 15 points to each skill, and keep in mind that you get to tag three skills at the beginning, giving each of them +15. So you need to add 15 points to ten skills, meaning 150 skill points. You'll manage that by level 9, leaving you 21 level-ups worth of skill points you don't really need.
What I'm trying to say is that maxing all skills, with Broken Steel installed, is fairly easy. Not quite inevitable but it's definitely not a big challenge either.
Let me try to make the skill math a bit easier.
Your target is all skills at 100. With 13 skills this means 1300 skill points.
Assumption 1 - You'll get all SPECIAL attributes to 10
Assumption 2 - You'll pick both Cyborg and Silent Running, which both give +10 to a skill.
Assumption 3 - You'll pick Comprehension.
Assumptions in place, let's do some counting.
29 level-ups for 20 skill points each: 580
322 books for 2 skill points each: 644
13 bubbleheads for 10 skill points each: 130
2 perks for 10 skill points each: 20
SPECIAL resulting in +25 to all skills: 325
Sum of all skill sources: 1699
What this means is that if you do all things the optimal way, you'll end up with almost 400 skill points you'll never get to use. That's no fun at all, so something less gamey is probably in order if you also want to have fun.
What I tend to do is pick some key skills that I don't care to be efficient about. I will max those skills ASAP with little regard to bubbleheads and books unless I happen to stumble over them. I'll perhaps "waste" as much as 40 skill points in such skills but I do so gladly, since 90 small guns or 100 lockpick does wonders to improve your character's abilities. Same with a high sneak or repair.
Wasting skills means I'll need to find relatively more books before maxing everything out at 100, but that's okay. It's as good a reason to explore places, it makes me traverse through the wasteland, and I do keep track of what books I've found and which books I haven't picked up yet. That's just me, though.
Now, regarding bubbleheads, the only bubbleheads you can't take until level 30 are the SPECIAL bubbleheads. The skill bubbleheads you should grap the first chance you get. There's never any reason not to, short of the consequences of stealing stuff when someone's looking at you. You also don't have to delay the main quest until level 30 because there's no SPECIAL bubblehead that will be made inaccessible by the MQ. The only one of those that even can become inaccessible is the Strength bubblehead, and it's pretty obvious what you shouldn't do if you know where that bubblehead is located.
It is correct that there are a few skillbooks that you can't get but the number is low. I'd personally take Comprehension just to max my book benefit sooner rather than later but it's not like the competition for a level 4 perk is all that tough anyway.
If you want to do this, you only need set your starting Intelligence to 7. You'll need about 150 skillbooks with Comprehension (and Educated for the extra points). It's a pain keeping track of the books you have in order to distribute your points evenly but it's something to do when you're bored.
Ghouls is more or less correct in this. You don't need more than Int 7, but why wouldn't you max it right away? And taking Educated, IMO, is a waste, even at level 4. It gives you, what, 75 skill points or so? What's the point? At level 30 you'll have every SPECIAL at 9 anyways, and all other skills than Int are retroactive, aren't they?
Regarding the pain it is to keep track of books you've found, I'd agree completely. Which is why I wrote every book into a spreadsheet which I'm keeping around on my laptop while playing. That way I know if I remembered to pick up this or that book. Took a few hours to type in all the darn books (or rather copy the locations from the Wiki) but those were hours well spent, catering to my borderline OCD.
Some people write fan-fics or make Enclave fanclubs, I tend to make spreadsheets to contain my notes.