New Building/hero mechanic: The Armoury
Preface: A partial implementation of 'heroes available in wars' ideas.
Ruled out: Part of this idea crosses into the ruled out area of new heroes. This proposes allowing a 3rd (or additional heroes) but capping active heroes to two. No specific hero is suggested (well, seriously anyway).
Summary:
Implement a new building called the Armoury. The building allows the upgrade and rest of heroes off pedestal. Pedestals are used for any hero, but there remain only 2 pedestals. New heroes are introduced and can substitute for upgrading or sleeping heroes. So for 'Pedestal A' you select and choose from a button for each available hero, whether Burger King, Arch Queen, or Doofas Bird.
You would be able to increase the number of heroes in the game, however it becomes a strategic decision which heroes to bring with you on defence or into battle. Only heroes on pedestals are available for battles/defence. Recharging heroes return to their pedestals to sleep, but can be swapped off into the armoury. The armourer becomes the place where all hero upgrades are managed.
Heroes in war: Upgrading heroes would remain unavailable for war, however if a third hero is implemented then the third hero can substitute for the upgrading hero. This means that the balance in war is less badly affected by the loss of heroes to upgrades. Upgrading heroes would still be available on defence in clanwars, so a different hero could be active on defence from that used in attack.
Hero recharge: Active heroes would continue to sleep on the pedestal but could be swapped off to complete their sleep in the armourer.
Armoury extra features: A designated building set aside for hero upgrades allows more interesting flexibility with the development of heroes. For instance, non-game affecting changes such as new skins for heroes or hero weapons in exchange for gems or gold. It may be possible to implement alternate abilities, so a hero ability (royal cloak) could be swapped out for an alternative (ham fisted: next attack does massive damage).
Heroes are a fantastic addition to the game, but have become really critical to the balance especially during war. They are such an important (balance, time consuming, upgrade cost) in later stages of the game that encouraging a limited degree of customisation could add a new bit of fun to the game at higher levels.