Buying a prebuilt system reputation and quality are far more important than picking certain hardware. Allow me to give you an example, just because they carry AMD and you get to pick your favorite CPU, that does NOT mean the motherboard included isn't bottom of the barrel. Without picking all the parts you are left wondering if (1) part here or there will cripple the rest of the system. Then if the company does allow you to pick your parts, then its not really a prebuilt is it, and you'll pay more for that custom setup.
This last year i ordered a few prebuilt systems for the big-wigs at work. Depending on what they wanted i ordered from various companies. If they wanted an above average system, but nothing too fancy i went with Gateway, for the money spent Gateway has some great setups. Now if they wanted a nicer, top of the line, professional system i went with Dell, for the additional money spent you get a PC that looks as nice as it runs. Even i'll admit the prebuilt Dell, black case, black 17" LCD, P4-1.8 the system runs as nice as it looks! But you do pay a bit more...
The average person won't be upgrading as often as most of us do, so it's better for them to get an all around quality system with a good warranty. Hate to say this but for a system that may never get opened for upgrading, cleaning, etc, i'd much rather have my friends get a cooler running Intel chip than AMD.