I never played SWSE, but I think the rule of "1 flaw = 1 talent/feat" is just too much! As some already noticed, you can take a flaw in something you'll never use (because it's not your area of expertise or another party member already has it), and get an unrelated feat to 'balance it'. It's not balance: buffing yourself to fight a horde of orcs is always better than cursing just a single one of them. My suggestion: flaws/feats that can only be taken at 1st level and look like these:
Book Worm
You spent so much time studying indoors that your body is not accostumed to physical stress.
Flaw: you are considered Inept in Athletics and Acrobatics (you dont get + 1/2 level while using these skills).
Benefit: you gain +2 at any two Knowledge skills.
Special: you can become Adept in said skills while retaining these benefits, by spending one feat slot.
Deset Dweller
All your life, you lived in an arid environment.
Flaw: you are considered Inept in any skill that relates to water, like swimming or maneuvering a boat (you dont get + 1/2 level while using these skills).
Benefit: you gain +2 at Survival skill checks whenever you are in an arid or deserted environment.
Special: you can overcome this flaw while retaining these benefits by spending one feat slot.
It's a small (but convincing) bonus, to a greater threat. I'm not sure how balanced this would be in SWSE, though.
As far as granularity, I never liked it. Character creation takes way too much time IMHO whenever you have to assign skill points. For those who like it, why not make every skill 'granular' (much like 3E), and each skill feat grants 5 skill points to spend on your class skills. As I said, I never played SWSE so I dont know if the math is right but if done correctly, you could even use both approaches in the same game: Players would use D&D 3E skill points, for maximum customization, and NPCs use SWSE skill feats, for faster gameplay.