A point of note - it is usually better to have one skill at eight and another at ten than two at nine. Your maximum effective skill is 1.5 multiplied by the base stat (i.e. no juice) rounded down, so making your base stats even numbers is highly recommended.
My problem, as a novice, is that I don't know yet the relative importance of heart, intelligence and charisma. I know intelligence is the basis for the majority of skills, but from reading around I guess that charisma is the basis for some key skills , used when brainwashing conservatives. The best attrinute scores are along the lines of:
HRT: 10 INT: 8 WIS: 1 CHA: 9 STR: 5 AGI: 8 HTH: 9 and
HRT: 10 INT: 9 WIS: 1 CHA: 8 STR: 5 AGI: 8 HTH: 9
You can get int to 10 with the basic three close together, but that costs a point in agility. which I'm as yet loathe to do.
I suppose apart from an initial point for Security to avoid needing lessons to start picking locks all skills are trainable in one way or another, so choosing which to start with is purely a matter of taste?
Mazur
It depends on what you want your founder to do. Here's what you use the skills for:
Strength: Axe, club and heavy weapons. A pretty useless skill - if you want a melee weapon, swords uses agility (a much better skill) and heavy weapons are so much harder to get and supply than rifles.
Agility: sword, knife, martial arts, all non-heavy firearms, stealth, dodge. This is an extremely important skill if your leader is doing anything dagnerous. High agility people are by far the most combat effective, due to the combination of so many weapon skills and dodge. The stealth is also extremely good.
Health: No skills. It is how hard your founder is to kill. I find it mostly useless, because if your founder is damaged enough for the difference between 8 and 9 health to be important, they're likely to bleed out or die from conservatives shortly after.
Intelligence: Lots of things. Of note are tailoring (a good money source) first aid, computers, security, and the interrogation skills. I usually try to get very high intelligence.
Wisdom: You don't want this.
Charisma: Only has three skills - disguise, persuasion and seduction. All of them are extremely important. Charisma can render any fighting unnecessary, as a good disguise and high charisma can mean bluffing out of every situation. Persusation varies in its usefulness - high values only come into play if you're trying to recruit conservatives, and there are plenty of good liberal recruits. I don't use seduction, but others use it to great effect.
Heart: Music and Art. A very high heart (15, achievable with 10 base) can allow you to pacify and recruit things like guard dogs. Given how good they are at detecting you, pacifying them is very useful.
Keep in mind that you can recruit other people to fill in for you leader's deficits, but none will have as high base stat total as the founder.
What stats you want to give depends on what role you want your leader to play. I don't like to risk my leader, so I go for high INT and CHA, recruiting others to do the dirty work and tailoring to fund them. If you want your leader to do solo missions the safest bet is to pump CHA for disguise and bluffing, with at least 10 heart. If you want your leader to take part in death squads, then pump agility all the way - your leader's heart doesn't have to be 10 base to be able to pacify dogs, as long as someone else in the squad has sufficiently high heart.
Also, the initial point in security isn't that hard to get - university classes at low skills are effective. You can also have meetings or dates with someone who has points in the skill to get trained in it.