edit: Bah, 8 posts while posting this? There's now some overlap with what has already been said.
Okay.
There are two discussions going on here.
The "let's change crystal" discussion and the "new mechanics discussion"
Ignoring the 'new mechanics discussion', how do we go about making crystal distinctly different from what we have? No consideration of what the crystal will be used for here, just how to make the resource distinct, as a resource.
Metal:
Infinite income limited only by the rate it can be gathered. No real penalty for losing metal harvesters.
Can be stockpiled to a reasonably high amount, no on-going costs once building a unit is finished.
Controls how fast you can build units.
Energy:
Infinite income resource limited by the number of systems controlled. Losing energy collectors can have immediate effects but no long term effects.
Can not be stockpiled and units have an on-going energy cost.
Controls the maximum size of the players fleet, if needed you can get more energy at the cost of metal, increasing your maximum fleet size at the expense of slower construction times for new units.
Asteroids (Spirecraft, if enabled)
Limited resource that allows the construction of new units, most that are not direct combat units and give you new options.
No on-going cost once built and no penalty to losing a system with unused asteroids in it.
So, how do we make Crystal distinct?
Well, both metal and energy already control the player's fleet size so crystal should probably not touch any of the current units.
However, I really like the fact that you can burn metal for more energy so there should be a conversion mechanic of some sort.
To prevent any units built from crystal from overshadowing your fleet, they should not be direct combat units, we already have our fleet for that. Rather, make the crystal units have abilities that are sideways to our fleet so it is now an apples-to-oranges comparison and a player will determine for themselves how much crystal they need in the game.
Actually, the more I think on this, the more this sounds like a resource for a new Fallen Spire type minor faction with crystal rather then city hubs as the resource it uses.
Maybe a "high-intellegence" neinzul allies with the player to free it's brethren from the AI's hands? (AI-Neinzul hybrids).
Actually, now that I think of it I'd rather you left the current resource profile in place and anything new in this regard was added to a new minor faction somehow like the Fallen Spire or the Ancient Shadows stuff.
I don't think there is anything wrong with the current model and the effort required to implement something new like this is going to be pretty major. Is the fact that metal and crystal are currently so similar that it is a weak mechanic? Yes. But the economy stuff is a side-show to the main game anyway and there is nothing actually wrong with it.
I think the fact that coming up with something to replace it is causing so much difficulty backs my case up here. I'd rather developer time was spend on new content or tweaking stuff that does have flaws as opposed to a weak mechanic that does not have flaws in it.
(I don't consider the fact that metal and crystal are basically the same except for the name a flaw, opinions may differ I suppose.)
D.