Here's my opinion based on numerous trips from LA to San Francisco or Sacramento for work. I found that the time on I-5 or Hwy 99 only varied by less than an hour if conditions were similar and no accidents.
Personally I prefer Hwy 99 because there is more to see along the way.
Hwy 99 does have more rough patches than I-5. The drawback on I-5 is the section Through Lost Hills and past Los Banos you end up slowed down by strings of trucks passing each other on the hills. This can go on for miles and miles. It get frustrating, just as you get a nice run at a hill a truck will pull out and slow you down. Hwy 99 isn't as hilly so this doesn't happen as often.