Maybe perks could be that your summons have better equipment like higher levels or enchantments. They could also have some of the magic perks whatever they are. Also, summoned equipment could have enchantments on them.
Another idea I had was if a summoned creature dies before its time is up then you get a portion of the magicka back. Also, things like getting a portion of the damage dealt by your summon as health or every kill they make extends their lifetime.
I just don't want them to be generic perks like +damage, +health, +time. Those should be inherent in the increase of your skill.
I agree, I think raising the skill alone should do more then simply allow you to do higher level summons. Since they took out spellmaking, How does one figure it he has the necessary skill to summon said creature?
I don't want to see *You need 75 Conjuration to summon this* Thats just...I'm not a fan.
So it should just be that every creature strength is based on your conjuration, and you can summon any that you can get your hands on. And like you said, Allowing perks to be for more unique effects on the summons.