I'm still pretty aware that there is a retooling effect in the game but it is not the same as designing a new ship type/class and all the time it will take before you can lay down that first hull. Retooling is something you must do at every naval yard every time you want to produce another ship type there.
I would also think that the prototyping/designing of the ship should be a research project and not a naval yard retooling effort. In my view you could do the research at the same time you perform the retooling. So it will not necessarily take more time but you would have to consider both time AND research. As you would in reality.
My suggestion were more of a reality sake than a game balance sake. I have seen many comment on these forums of features being included for the sake of reality, so why not consider this if it could easily be included without adding much additional micromanagement. One more research project for a single ship is not that much extra you have to do.
Sure, research will take a little longer... personally I don't see anything wrong in that in principle. I like when things take a long time.