This is why we use non-dimensional flow in sizing calculations.
This is why we use non-dimensional mass flow in many sizing calculations.
Rockets should be designed with chamber pressure as an input. This, in combination with throat area, sets the non-dimensional mass flow, which allows pump sizing to be decoupled from thrust chamber stressing.
Rockets add the complication that the speed of sound in the throat is driven by the mean molecular mass of the products of combustion, which is f(mixture ratio, pressure, temperature) due to dissociation effects.
A reasonable way to tackle this would be to use a code like
CEA; it's actually got a module for calculating theoretical rocket performance, so it's a relatively simple job to port it (there are some bugs lurking in the FORTRAN which may be squashed along the way). This has the advantage that it would be possible to use arbitrary combinations of propellants, so we could play with
tripropellant rockets.
Fuel & oxidizer pumps should be sized independently, because they are often very different & have different materials constraints. This can be done according to the guidelines in the monograph I linked earlier.
Suitable generic pump maps from the monograph should be used for matching. The user should drag the design point around the map. There should be an option to drive the pumps electrically or with a turbine. If the pump is electric then the engine has an electrical power requirement set by the design-point power requirement of the pumps (& will have to carry motors around with it), but the running line can be user-defined. This probably allows for deeper throttling & greatly simplifies the starting problem.
If the pump is driven by a turbine then a generic turbine map should be used to help define a running line which may then be matched to the constraint imposed by the throat. It is likely that surge or similar will limit deep throttling. In this case, there should be the option to extract electrical power from the turbine at the expense of weight & cycle efficiency / specific impulse. This would probably permit some classes of ship to have much smaller generators. The constraint that rocket thrust be applied when large electrical loads need to be serviced may not really be a limitation for a combat ship whose electrical loads are weapon-related, because it will probably want to dodge enemy fire. This would also permit RL10-type engines to grow larger by getting around their pump power limitations.
Starting can either be pyrotechnic (simple, but scales badly if multiple restarts are required) or electric. The requirement is to get the pumps up to the bottom of their running lines in some relatively short period (e.g. 0.1 s), which can be calculated based upon pump mass & dimensions. From a systems engineering perspective, dependence upon electrical power for starting is a vulnerability.
Regenerative engines' turbopumps may be driven by the heat they extract from cooling the cycle; this limits their size because the eventually run out of surface area at larger sizes. This is why the RL10 isn't bigger. At larger sizes, additional pump power has to come from somewhere else (e.g. a pre-burner or expander cycle).
It is worth noting again that radiator sizing in the game is pessimistic (especially for missiles) because the obvious thing to do is dump heat to propellant & throw it away in the rocket exhaust. This is very attractive in short duration applications (e.g. missiles) but limits time on station because eventually the fuel runs out of thermal capacity & has to be dumped (cryogenics will boil away; things like RP-1 will eventually coke). Additional fun can be had staving this endurance limit off by using cryocoolers (upon which Mr Carnot does not smile).
Boil-off may significantly limit the performance of some designs with poor surface-area-to-volume ratios, especially close to the Sun. I would expect to see gold foil outer layers appear on many designs for this reason, & it is likely that this will impose serious limitations on the use of cryogenics in long duration applications such as those seen in some of the campaign missions.