I'm on my third game, making the jump to a gigantic map. There's still a number of things I'm learning about the game and I was probably within a year of being absorbed into the Arcean sprawl before I retooled my factories to start producing mass quantities of ships.
I mention this because on the larger maps, there isn't a single stock/core ship that is useful at any distance from your area of control. Sometimes your nearest neighbor is too far away for the stock freighters to reach them and you have to design your own that can get the job done.
Also, the game is designed for flexibility. Your AI opponents will constantly switch weapon types and a stock ship won't have the flexibility to use the most effective weapons/defenses for the job.
For instance: I'm stuck in one corner right now and my best chance to expand is to attack in the opposite corner. With the technology I had at the time, I designed a constructor with a range of 6.5 and speed 5. That was just enough to get it into an open area between to other races so I could build a non-imposing economy starbase. How did I know where to put the constructor? Again, I built a scout ship that could almost cross the entire galaxy. Even then it just barely had the range to scout out a good location for the economy starbase. Sending the constructor took over 20 turns and by time the base was built I had enough technology to build large hull ships with the range to invade. Built long range troop transports too. I sent a convoy of near 18 large ships and 14 troop transports moving speed 9 across the only empty part of the map (again 20+ turn trip) and took 8 planets in 3 turns once I got there. Now that I've a foothold, I'll still keep the engines on to keep the ships from obsoleting during the trip, but redesign them with less support modules and throw on another weapon. With another tech, I'll redo my long range transport with even more speed and send the new ones across the galaxy at speed 13.
There is no way a stock ship would have allowed me to do any of that.
The other comments are spot on: you don't need to spend 8 hours designing a fancy ship unless you really want to. I'll take maybe 15 minutes to find the best combination for a specialty need, name it, save it, build it. If all I'm doing is updating engines and weapons, it's less than 5 minutes. The neat thing is, once you've made these ships, the next time you play the same race, they will become available as you get the technology.....just like you were expecting the stock ships to do.
Designing your own ships is a huge strategic advantage over other 4x games I've played.
Just my 2 cents.