More flexible Mods- A few ideas
Depending on the rarity of the mod, it recharges the portal to combat the decay. So lower panels can't prevent the decay completely but only slow it down.
The negative aspect to prevent it from being too powerful would be additional leakage of xm around the portal so that an attacker would also benefit
To counter simple drive-by destructions by high level agents i think a lightning rod that transfers a high amount of incoming damage to linked portals would be great.
This forces methodical war plans and surgical strikes from the edges of a field . People work from the outside in and go for the weak portals first to take the defenses down.
Sometimes you pull your hair out over some stupid mod that doesn't fit your plans. Like a link amplifier that blocks the slot but you are surrounded by fields and links and can't make any use oif it from within a city centre.
Maybe have some risk associated with it like you can accidentally remove an additional mod that you didn't intent to or damage the slot in the process for a while.