US subs, now with real fish.

There were also other reasons to use a cruiser as flagship, aside from the fact that battleships tend to attract the most gunfire: Cruisers and destroyers were generally a closer to the fight, so the crews of that one ship could directly tell the admiral where everyone was by their own instruments or spotters, alone. After having the flag transferred back to Yamato, for example, was when the infamous Battle Off Samar happened, when the Admiral for the Japanese side mistook destroyers for heavy cruisers and escort carriers for fleet carriers... which wasn't helped by the fact that Yamato had been forced to pull back from the engagement to evade torpedoes and was much further away from the action than all the rest of his ships.

With that said, destroyers were generally too small to fit all of an admiral's staff plus extra equipment for managing a fleet without compromising some other functions, plus they had little to no protection for the admiral, so cruisers were a good fit for an admiral.

Ooyodo, here, was, in fact, explicitly designed to be a flagship, which is why she didn't have torpedoes (why would the admiral's flagship perform such a brash maneuver) but did have an extended hull to help fit all those extra meeting rooms and such inside her armored hull space.