If I understand correctly what YG is seeking, the requirements are for a special cruiser bonus that a) applies only to cruisers and to no other ship type; b) that does not involve a combined-arms pairing between a cruiser and another unit; c) that is historically accurate, both in terms of the technical features of WWII cruisers and their actual use in that war; and d) which does not involve an IPC price adjustment.
Frankly, I can’t think of any historically accurate things about cruisers that would fit all those requirements. At best, there might be things that could be bent or stretched to partially fulfil what’s being looked for. One idea I’ve already mentioned is the concept of giving cruisers some kind of equivalent to the OOB blitzing ability of tanks, to reflect the combination of speed and long range which cruisers offered. Another possibility – which someone would have to develop more fully, because I don’t know exactly how this concept could be translated into house rule terms – would be the following one. Task force commanders often (but not invariably) commanded their forces from a carrier or a battleship, or sometimes from a cruiser. At Midway, for example, Yamamoto commanded his Main Body from a battleship, and most of the other admirals (on both sides) commanded from carriers. Fletcher and Nagumo both lost their flagships (carriers in both cases) to battle damage, and both admirals transferred their flags to cruisers – the Astoria and the Tone, if memory serves.
So perhaps, as a stretch of this anecdote, there could be a HR stating that, only once per battle, if a player’s battleship or carrier is damaged but not initially sunk (2 hits being required to sink), it can be presumed that the force’s commanding admiral had been using that vessel as a flagship and that he has now transferred his flag to an adjoining cruiser (if there is one, of course, which would be the incentive to buy one ahead of time). This transfer of the flag would confer some sort of mitigation-of-damage factor that would offset the BB/CV hit in some way. I don’t know what that offsetting advantage could be, however; our resident house rule creators would have to see if they can come up with something. The answer would probably be easy if the OOB rules used commander pieces, but alas they don’t.
The reason this concept is “a stretch”, by the way, is that flag transfers didn’t always operate as I’ve described. At Leyte Gulf, for example, it worked in the opposite direction: when Kurita lost his flagship, which was a cruiser, he transferred to a battleship.