Wait, I've got it!
Chakra-activated runic mine
An explosive rune that, once fully activated, goes off instantly if a large chakra source enters the zone.
Substitution-activated runic mine
And explosive rune that, once fully activated, goes off instantly if someone substitutes into or out of the zone.
If this works, we can also try to deploy the time-slowing runes with the same mechanism.
EDIT:
Unsummoning Anchor
while active, causes summoners who unsummon from the 7th path to reappear next to the rune, instead of the location they reverse-summoned away from
Chakra Shredder Rune
a rune(or array of runes) that rips apart chakra systems and chakra constructs it's area of effect.
we expect this would destroy: Konan's Paper form, Sasori's chakra strings, all Shadow Clones, all Summons, most justsu that make a chakra constructs or have complex effects that linger outside the human body.
If it turns out this rune also shreds chakra systems *inside* people, that's fine to I guess, but not a design goal.
Chakra Shredder Pulse
a hopefully-easier version of the Chakra Shredder Rune that acts kind of like an explosive; short-lived, only useable once, and big AoE.
EDIT EDIT:
"Let's fuck with Sealmasters" Rune
Activates all conventional seals in a large area around the Rune.
This can either be continuous or a one-off burst, Whatever Hazoupilot thinks is easier.
"Let's fuck with Sealmasters who aren't us" Rune
Like the "Let's fuck with Sealmasters" Rune, but designed not to trigger seals designed with a specific unconventional feature/pattern in their activation.
Sealmasters who know that specific pattern could research seals(or seal variants) designed to not be triggered by this rune.