The pre-built ships included with each civilization provide the player what they need to play and win games. Custom ships on the other hand provide people with an opportunity to tweak ships to fit their play style. I personally play with a mix of both. I usually roll with the pre-built ships in the beginning and start tweaking my designs as I progress.

Custom ships can help a lot....depending on the individual game.

What I have notices is that the "stock" ships, are based on what weapon techs you research first.    So if you research beam weapons, and missile defense....you will get default ships with good defense against missiles, and beam weapons for offense.

However if later in the game you need to fight an enemy who also uses beam weapons....you then research beam defenses....but your default ships will still have mostly missile defenses.    So at this point you will REALLY BENEFIET from creating a new ship which has ONLY beam defenses.  (ie you're not wasting "space" on missile defenses that you dont need)

Other times I might create a new ship like a constructor or transport which has good engines so that I can get them where they are needed quickly.