Agility is 6 due to perks requiring this value, and an implant can raise it to 7.
Intelligence is 6, but at level 2 I recommend you use intense training to raise it to 7, and an implant later on brings the final value to 8, which is more than enough to be able to max most if not all your skills.
The only other thing affected by charisma is your companion's nerve, which really isn't that important. Even with a starting value of one, it isn't hard to increase your speech or barter to a acceptable level. Charisma is 1 because it is the most useless stat in my opinion. You can choose to get an implant for each of your SPECIAL stats, or you can ignore charisma and/or endurance in favor of the increased DT and health regen. Endurance is also at 7 for implant reasons. Add any hat with +1 perception and an implant, and you've got yourself a perfect 10. Also, with the four eyes trait your perception will be 6 without glasses, and 8 with. Perception is at 7 because it is one of the determining factors of your energy weapon skill.