We only go custom if there's a need. From working in the industry, pre-builds are often built to a price point as the manufacturer buys parts in bulk, and will get value for money (or otherwise take it as extra profit).

Also technology and innovation goes into pre-builds- so you want to ride the wheels that won Stage X of TDF- well so you can.

However of course pre-builds have a huge draw back. They often are built with a weight limit, usually 90kg. If you weigh more than this you are setting yourself up for problems with the wheel- as my DH found out. Cracking rims and breaking spokes etc.

So getting custom wheels is often required if you have special circumstances- you are heavy, you want a wheel for a special function, like tandeming, or you are small but require a performance 26" wheel for your bike (as options are very limited).

Going custom doesn't always mean getting better- it depends on who is building them and what kind of "care" package you get afterwards. A poor build or selection of parts will not make a good wheel, and if the builder isn't able or doesn't want to give you free adjustments, well that means extra dollars. Pre-builds are at least supported by a manufacturer who will repair or often swap the wheels out- but also this can go wrong as well!

I personally don't think either way is better- it really just depends on what your needs are and how much you have to spend.