I've always thought we should focus on defensive runes.
It's just obviously what they are better at, what with then not being able to move and such.
I want to bring up the idea of the speed limiting rune again. It is wind aspected. It provides exponential resistance to air movement within its zone. Ideally it could be a tunable effect at inscription time. It would effectively prevent or impose a massive stamina penalty to ninja speed movement and projectile weapons, while also significantly reducing the effect of explosives. Anything trying to go fast would have to face the issue of pushing the air out of the way when the air does not want to go fast.
We want to target air only so peoples blood does not get slowed in their veins.
This would serve as a pretty strong counter to a large variety of the city killer techniques we know of. It could be tuned so that at civilian speeds there is nearly no effect except sneezing & coughing being extraordinarily uncomfortable. Maybe a bit of trouble during fast heavy breathing. Essentially a passive defense.
So at an estimate, some sort of massive Air Dome (or equivalent) to protect all Konoha, and some sort of long-ranged chakdar that responds to and can track high (ninja-level) chakra density.
An air dome can be bypassed or broken and can only be activated once you notice an attack approaching, if there is one thing we should learn from the multiple times cities have been attacked during this game, it's that an active defense is useless if you can't see them coming.
Think about it.
When has there been a major time we were attacked or were attacking a city where the city got enough advanced warning to activate a shield?
Not during the tunneling incident.
Not when we nuke isan.
We need something passive that can be left active all the time.