Gates
Gate customization is broken. It's excessively difficult to coordinate enough of the right colors to even start experimenting in an intelligent way. Anything you do is quickly buried by other players who add all their crystals. It's only going to get worse with a bigger player base.
To fix the problem, allow players (or guilds) to start their own gates. Starting a gate would cost Energy and Crowns, but if it was popular give you a good chance at making money on the deal.
Once it's created, let the person who starts a gate you set the rules for allowed minerals. For instance, you could restrict your gate to only accept Yellow and Red ore. One way this could be done is with ratio caps:
Green: 0
Yellow: 2
Red: 1
Blue: 0
Purple: 0
In this example, you could deposit as much Yellow as you wanted, no Green, Blue or Purple, and Red up to half of the volume of the Yellow. Allow the gate owner to modify the rules over time to tweak the gate as it's being built.
This way people could more easily customize and experiment with gate creation. Additionally, the playerbase will more easily customize the game to create the levels they want to play most.
You don't like how something works so it's broken?
I dont' mind your ideas or explanation, but calling it broken is silly.
You see, the idea is to use dusk drops. Let everyone do whatever they want with the gate, then on the last day you come with your guild or friends, drop 1000 blue minerals an 4 dusk drops, and now all the levels near the core should be blue. It kind of harms players that want the early or middle section of a gate to be of a certain color though.

The last post in my thread might have a few remedies to this problem, although I do like the idea of Guild Gates. I think they would make getting public gates co-ordinated even more difficult than it is now.
They would need to be introduced once the game has a bit more population or something, otherwise only Guilds would have Corebound gates.
Not to mention that from the Guildhall, there's no clear point at which they would start, there'd need to be an entirely new mechanic for them.
On the opposite end of that, I think giving specific people control over public Gates might lead to even less productivity. If people don't agree on the distribution of a gate, no deposits. If the distributions in other gates don't allow for you to get the required mineral in the amounts needed to create a gate that goes through Tier 1~Tier 2 let alone to the Core, it would put a halt on Gates until the next one.
Or how competitive the game would become if at 8PM everyone logged on to try and get in first to set distribution.
It would be rage inducing madness.
The system just needs more improvements in the way the tray system balances itself, because it's pretty clear it's not working out the way it is now.
People are picking up enormous amounts of minerals and not depositing them.
I like your suggestion, it's interesting. In the meanwhile you could experiment by adding a dusk drop whenever you're depositing minerals? That way you know the bottom levels largely came from your own deposits and as such are a result of your experimentation.