Towers and Neutral Weapons
I feel like towers don't mean enough. For example in Dota 2 or Heroes of the Storm if a tower is killed it's a pretty big deal. You can't push as hard in that lane and it's easier to be pushed into whereas in Atlas it's just one giant push into the enemy instead of a steady breakdown of the enemies defenses that eventually leads to the collapse of the enemy Nexus.
This game is unique though in that you can rebuild towers which probably leads to them having to be weak so that the game doesn't drag on for too long.
Neutral weapons feel too strong the way towers are right now. They are easily spammed and melt towers when this happens.
I think a possible solution is that towers can be buffed in terms of HP while also increasing their cost up from 2 gems to 5, 6, or even 7 gems each. Neutral weapons could be nerfed or have their costs increased.
Gem collection is a big part of this. Gems with gem expansions get players a lot of gems which causes the spamming of weapons into towers. Gem collection could be changed to help solve this either by decreasing the collection rate. Map design to make them more vulnerable is also an option.