This idea has been rattling around in my head for years. Basically, it always bugged me that prototype double heat sinks couldn't be installed in the engine for "reasons", while the regulars could be. So it strikes me that instead of that odd prohibition, why not simply just make them half a ton, and take up two critical spaces? To get two heat, you need one ton, and four criticals, but you can stuff a single one in a leg. The whole series would look something like this:
Type I Heat Sink (normal, single heat sink): 1.0 ton, 1 heat, 1 crit, can fit in the engine as normal
Type II Heat Sink (prototype double heat sink): 0.5 ton, 1 heat, 2 crits, can fit in the engine like normal (but that only gets you 10 free heat, and the ones outside the engine take up twice as many crits)
Type III Heat Sink (IS double heat sink): 1.0 ton, 2 heat, 3 crits, can fit in the engine
Type IV Heat Sink (clan double heat sink): 1.0 ton, 2 heat, 2 crits, can fit in the engine
A further option would be to allow them to be installed alongside Type I or Type III heat sinks (but not both at the same time), though this removes the requirement for all the heat sinks to be the same (which I think is more consistent).