First off, I don't know if it has already been suggested.
Multiple Key Usage
It's annoying to carry around a shitload of keys all the time for the town (often using more than one gate), personal gates and maybe even the ones for a partner town.
The suggestion is easy, make the player be able to decide for which gates a key fits. For example, one wall around a city, 4 gates. Being able to decide the key fitting in all the 4 gates you can reduce the number of keys to carry around from 4 to 1. Same with personal gates, some kind of universal key. To prevent from validating keys for a foreign gate it's only possible to validate a key for the gate the keyholder personally built. For this purpose every gate is registered to the one who built it, and thus this person is the only one who can validate keys for this very gate. The key with all his registered gates can be multiplied as usual.
Keyrings
If this is way too much work to do, simply create an item which serves as a container for keys and can be placed on the characters gear screen. It can hold up to 10 keys and all the keys (and only keys) can be placed inside.