Summons having all their cooldowns tied together does make sense.
How about making a consequence for slain summons?
e.g. apply status effect to summoner that prolongs the summon cooldown, or summons progressively weaker summons (strong ones won't answer your call!), or summon has a chance of turning on you.
The purpose is to encourage keeping the summon alive via healing or buffing.
I'm not sure that's a terribly useful idea. It doesn't seem to address, say four characters, with one summon each, tanking all the enemy hits. Applying a penalty for a summon dying, given the existence of Destroy Summon, which can't be defended against at all, has the ring of unfairness.
