Prebuilt;
for people who don't have time or the option to scope out parts and build it themselves, or even a store that allows you to hand pick your parts. They might end up cutting corners to make a profit. You might void warranty if tampering with the build while under warranty period. Chances of upgrade can be limited, depending on the platform.
Self built;
You know what goes into your builds, hand picked components/parts. Room for upgrade as you see fit, you'll be informed of what you can and cannot do to your build later down the road as you research into your parts. Since you don't need to factor in a build cost, chances of you putting quality components without a surcharge is minimal. Self gratifying feeling of building something by yourself, starting from researching of parts and ending with the PC's assembly.
This has been stated ad nauseum(no offense meant) over the past decade that I've been here. I'm sure there are other points I've left out but you can search across our forums on the benefits of a custom built system.