Beacon That Emits an Short-Range, Selectable Aura Effect

The beacon's footprint would be small. 2x2. A small, colored gem(s) on top of the structure would indicate the effect it currently has on its resident base.

The area of its effects would also be small. Perhaps as small as the Wizard Tower's attack radius - if not smaller.

The small size and modest area of control will give rise to many new interesting base designs. Players would need to choose where to place it (and the other items in their bases) depending on how they are using it at the moment.

The beacon/totem would emit an short-ranged aura over the area it controls. The aura is selected and can be altered by the player at any time. In order to keep players from abusing the effects or potentially unbalancing an aspect of the game, the beacon takes (perhaps) 2 hours to switch its effect. The old effect would remain around the beacon until the waiting period has ended. Players can spend gems to eliminate/accelerate this waiting period, of course.

Some possible effects might be:
Gold Boost: Mines within the beacon's radius are 5-10% more efficient.
Elixir Boost: Collectors within the beacon's radius are 5-10% more efficient.
Defensive Boost: Defensive units inside the small radius are 10-15% more effective. The attacking player need not fight them there, of course.
Slow Effect: Enemy units are 10% slower.
Necromancy: Enemy units perishing inside the radius have a small chance of returning as a skeleton on the defending player's side.
Armor Plating: Buildings and walls take slightly less damage inside the radius.
Healing Stream: Units and buildings inside the zone are healed for a VERY small amount constantly.
Bugle Call: 5% off unit build times inside the radius.
Graverobber: Tombstones collected inside the beacon also give 10 gold.

As I have mentioned, these are just possibilities. There are many more, I am sure. Not all of them are desirable, BUT the core concept is to give the players a flexible (but NOT overpowered) tool to slightly customize and personalize their bases based on their playing styles or needs at a given time.