All of the pre-made kits basically have decided on the compromises that are made for you.
Assembling your own system allows YOU to choose the compromises.
And there are always compromises-
even choosing whether you want max cooling and will accept noise is a compromise.....
SO, yes: it is usually better to build your own.
There ARE a few things about kits that you can NOT get this way:
Ease of shopping/assembly- kits usually include everything you need to water cool.
Limited choices.
Seriously- some kits are ok and will perform decently- Asetek, Corsair and Koolance Exos are the ones that pop into my mind offhand. But none of them will get you temps as low OR a system that is as quiet as a home built.
And they usually cost more too.
Building your own does take a bit more time to decide which components and how to fit them all together, but it is worth it to most of the members here that watercool.