These special elements would fall under the greater umbrella of planetary specials amirite? I think the limit is when your elements start behaving and looking like other elements. For planetary specials the limit could be as high as 30 unique objects, maybe 7 of them would be special mineral resources. I think the numbers depend on how imaginative you're willing to be. I'm not aware of any hard-coded limits.
Yes, and no. Naturally occuring deposits would be planetary specials, or perhaps associated with a different sort of stellar object. But I think that to balance them it'd be best to make them synthesizable. Afterall, you could synthesize Xentronium in the MoO games. :p ideally this would be accomplished by building something that simulates the effect of the special.
I keep going back to the way BotF handled Dilithium as an example. But it's a GOOD example of the basic idea, well, in some ways. Dilithium can be synthesized, but it's not cheap. The primary source is naturally occuring dilithium deposits, IE specials that spawn on stars. (Everyone's homeworld has one.) Oddly it was the only stellar special in the game, then again BotF each special had certain places where you'd find it and nowhere else. As an example, jungle planets often had food bonuses, but never energy production. Terran planets (class-m)sometimes had food, but were the primary source of a "hidden" special that greatly increased the system's population growth. Volcanic, "class-Y", often had energy bonuses, but never food, and rarely had a decent pop growth rate. but that's kinda wandering off the topic. The reason I'm mentioning it is, that was pretty much the sum total of system specials.
Dilithium was associated with the star, even though the TV show showed it occuring elsewhere.
Anyways, WHERE the special is located isn't much of an issue. The topic at hand is how many types.
Obviously Xentronium is a must have. It fits nicely with anything involving armor.
What other areas of the game are there that could be enhanced by dicovering a rare element?
Weapons, we might even be able to split this into multiple items. One of the previously mentioned ideas "Zeon gas" would have energy transfer enhancing properties. Using it in ships would increase beam weapon output, energy conservation, and somewhat improve engine performance. This of course leaves room for another element that has different properties that can be used to augment weapons in some way. erm, actually Xentronium falls into that category too as it'd make sense to have the option of armoring missiles with Xentronium casings. But neither idea would increase the DAMAGE of missiles....
*looks at previous pages...* I made a list!
Q-Zeon(zeon was a smidge too already used): Primary use: augments weapons power/accuracy; Secondary uses: increase efficiency of engines, allows you to use it to add "kills crew" to your beam(?) weapons(maybe seperate research projects for various weapon types?)
Surillium: primary uses: Increase industrial efficiency; Secondary uses: improve shielding, improve ship power conservation
Those would be basic items that anyone can use effectively. Next are special elements that are primarily beneficial to specific race types. Four to be precise.
Biomethium: Primary use: augments biotech; secondary use: allows non-biotech structures/devices to mimic the properties of biotech(at the unaugmented level).
Trinatrium: Primary use: augment crystalline tech; secondary use: allows non-crystal tech structures/devices to mimic the properties of crystal tech(at the unaugmented level).
Syntritium: Primary use: augment solid energy tech; Secondary use: (see above)
Voldium-X: Primary use: Augment Transphasic tech; secondary use: ditto...
Obviously the four related to racial tech are less useful, but it'd be interesting to have a racial advantage that gives you a supply of a certain material on your homeworld.
Another idea I came up with is a material that improves construction times.
Making it easy to manage them is (to me) easy. Normal "day-to-day" production doesn't care about whether they exist or not. Therefore adding them to the main interface would be counterproductive. I'd have a small pop-up window hold a list of the materials you have access to/stockpiles of and the extraction rates of each. IMO it'd be the ideal middle ground between presenting the information and not overloading with the info.