I generally aim for a sort of tiered approach to ship design, combined with how I direct my research.
I mainly create a completely new design every time I develop new engines - those are large, expensive, and use valuable minerals (gallicite), so I almost never refit with new engines. I also almost never refit armor or shield generators - a lot of cost for a marginal improvement, and from a purely pragmatic perspective if the older ships are easier to destroy, they're also less valuable. So in an ideal world, I try to concentrate research so I get my new engine, armor, and shields done at a similar time to base the new design on.
Once I have my new design, I focus on researching things I will upgrade. Sensors, fire controls, and ECM are obvious candidates for upgrades, as they give a large performance increase for a small refit cost. Heavy beam weapons are another example - range is king in beam combat, so a new heavy railgun with 30,000 km longer range is something I consider worth the refit cost, as are magazines, though in both cases I try to keep ship tonnage as close as possible to minimize refit costs (and changes to the armor). As these finish I create a (b) variant, or even (c) and (d), to refit older ships to and new ones are built to that standard to begin with.
That leaves missile launchers and point defense weapons as somewhere in the middle - they're reasonably large and expensive to replace, but less so than engines or armor, and are generally pretty useful even at lower tech levels purely by weight of numbers. I may refit these components or I may not, mostly depending on opportunity costs (IE if I'm trying to expand my navy anyways I'll just build new ones, whereas if I'm content with my current forces I'll usually just pay to upgrade).
Then when I develop new engines/armor/shields the cycle begins again, with a II (or III, IV, etc) model utilizing those upgrades (new generations are also usually larger than the previous one). The b or c models of the older generation stick around for awhile, usually formed into their own fleets so they don't slow down newer, faster ships, but they don't usually get new refits after that point (why spend money on new fire controls for older ships when you could build new, faster ships?). I'd say that they get the less important jobs like guarding frontier colonies but that would be a lie - since I know I'm going to scrap the older ships eventually they usually get grabbed for the most dangerous assignments, like jump point assaults or investigating destroyed survey ships. I'm very ruthlessly pragmatic that way, and if I were doing more RPing I'd probably place a higher value on their commanders and crew.
