I also am with Fidelity and the flat rate is great. I too am irritated with the 9,999 as the max limit to buy without calling. Out of laziness and stupidity, I paid around $400 in fees to get all the share I have. That could have landed me 40,000 more shares.
If your account is coded for penny stocks there, you can buy or sell millions of shares at a time online if you want. I never ran into any of that limit that you mentioned...