Agreed. The process by which you fortify gyms is broken. Leveling up your gym is very time-consuming and can too easily be undone, especially by other players nearby. There needs to be a better way to handle gyms and battles that scales with local user activity... perhaps a shunt to a PvP mode that grants the winner or the winner's color a certain amount of exclusive access time to fortify.
The game is not similar enough to Ingress for the existing tit-for-tat ideas to work. Fire XMPs <=> Gym Battle; Add Resonators to Portal <=> Put Champion on Gym. Where's the equivalent of shields or key-based recharging at a distance? Why can't I buff my pokemon stationed on a gym (or the gym itself) with items after an alert that the gym is being battled?