"But wait Joker! Don't slots 1-3 already get crystal bonuses?"
Yes, but what I'm suggesting is different. Crystal mines are the only mines that increase in cost by 1.6x per level instead of 1.5x. This means in late game, upgrading crystal mines gets prohibitively expensive, as the increased production is not justified by the cost of the mine, resulting in mines that are 5-6 levels lower than metal mines, and 3-4 levels lower than deut mines.
In order to make slots 1-3 more appealing for miners, GF added a 30%/20%/10% bonus scheme, but this still fails to make the slots competitive, the additional gains still do not justify the cost, and no reasonable miner would take low level slots.
What it needs to become competitive is a percentage increase per level, to bring it closer to the 1.5/1.1 cost to production ratio per level for metal/deut.
Instead of the 30%/20%/10% bonuses, I propose slots 1-3 receive bonus production per level of mines in the amounts of 2.5%/2.3%/2%. In these slots, instead of production increasing at 10% per mine level, it would increase at 12.5%/12.3%/12%.
These per-level bonuses become equivalent to a 30% bonus at levels 10.6/11.5/13.2, and at level 40 mines, are equivalent to 2.685x/2.48x/2.21x current production.
Note this still is not overpowering crystal mines, they are still less cost effective to build than metal/deut mines. In order to give them the same cost effectiveness, the bonus would have to be increased to 1.1 / 1.5 * 1.6 - 1.1 = 7.3%, but given crystal mines lower base cost, approaching that number would give a stronger advantage to crystal mines.
Per my calculations, this would make slot 1 competitive in late game with slot 8 and 15 in terms of production, which seems more balanced overall.