I'm looking at the Mod info, but so far I'm still not 'getting' some concepts yet - maybe someone brighter than myself can do some testbed ideas for these and see how they work - I consider this to all be inter-related, but most of it could be done individually.
I am mulling over several interrelated ideas about how mines, anomalies, and at least some ethical "dilemma's" work and I think this could be reworked into something more cohesive, and perhaps less (to my mind) unbalancing.
1) The AI's should be tweaked to go after anomalies more. The game I'm on, I am so far ahead of the AI's they're never going to catch up, and it's basically because I like long games and have been eating anomalies up the entire time. For a player to let me get away with this would be foolish, and the same applies to an AI. I only have five scouts, but they have massive warp drives at this point and I get 99% of the anomalies that occur out there. My fighters can toast their battlecruisers - That just ain't right - {G}.
2) Anomalies and mines should be *less* useful in balance. I can think of two ways to do this, and a combination would be better.
2-A) For both anomalies and mines, I think it would be good to have a building required to make use of them on a planet - I'm thinking two buildings - Say a building "Advanced Research Center" that would apply the benefits of a research mine to a planet, Advanced Military Center would apply the benefits of the military mines to vessels built on that planet, and so on. Ideally, I would go so far as to say only such center per planet - I was actually considering the possibility they could be an advanced form of starport - i.e., the starport would have the special facilities for handling the mined resource, and only those planets would get that advantage. But I'm not sure that makes sense in all cases, particularly since not all anomalies would stack well with all mined resources.
Because that would be the more advanced version - A 'once per civ' upgrade for a center 'authorized' to handle research materials gathered from specific types of anomalies - Your anomaly research center would apply the bonuses from research anomalies to a planet, your military anomalies research center would apply the bonuses from those anomalies to ships built there, et cetera. I don't think all anomalies should work that way - it makes no sense to the '+ x bc' anomalies, and the espionage anomalies are inherently empire wide - you might want a specific Espionage Center for that, or simply roll it into the Political Capital building for that and be done.
2-

Can Anomalies be used to present a specific technology that, in combination with known technology, could be used as requirements for other technologies, improvements, or items? This could be as in depth as a new, full tech tree to explore, not accessible from the standard trees, but interacting with them - the neatest version I can think of, not having TA yet, would be something specific technology that unlocked other insights in the racial tech trees, but it could be simpler thatn that - say, requiring giving an anomaly technology like the one in

above before developing Xinathium.
2-C) Some Anomaly materials (Particularly empire wide benefits that aren't associated with a specific research facility) anomalies should have a research cost to them. I could see this using the ethics question screen for something like "This ancient ship is dead, but even it's hull shows signs of manufacturing processes that could increases the strength of even our relatively primitive materials - it would cost perhaps 50 bc to move this from theory to practice - should we do this, or should we scuttle the ship to prevent it falling into enemy hands?". I'm not sure if there is a better way to do this, but it *should* be a choice, rather than a 50 bc debit someone can't afford at a given moment.
Which brings up -->
3) Anomalies should be one of the items that brings up 'ethical dilemmas' and unlock some mega events, perhaps based on your choices in them, even after you've chosen an ethical philosophy.
Now, in general, I think the ethical dilemmas are not terribly well done - I find it problematic the way they alway make it beneficial to be evil, although evil, neutral, and good are (it seems to me) balanced internally as to game balance in other ways. If you're going to be evil, I'd put off the decision forever, if I'm going to be good, I'd do it fast, and the qualities of 'Evil' and 'Good' seem to equate to "Ming the Merciless school of Employee Relations" and "Me Lawful Stupid Paladin" - Which is not entirely uncool, if I'm going to be evil I *want* to be Ming the Merciless, but I also want to be "Exploring Brave New Worlds . . ." style good, not Lawful Stupid - {G} - and surely these can both be better typified by ethical dilemmas that are trade offs for your civilization, rather than "I can't shoot straight, I must be the good guy?"
Taking all that into consideration,
3-A) If they were balanced correctly, they shouldn't make a difference to when you picked a civilizations philosophy if they did stop, which in turn means that they shouldn't be considered dilemma's, they should be opportunities. And those opportiunities shouldn't stop just because you're committed to a philosophy now. I'm a good person, and yet the universe still gives me these decisions to make. Why does my civilization get off scott free once they've made that decision?
3-

It seems to me a reasonable percentage of anomalies should be hooked into those opportunities. There seems to me to a fair amount of sane decision making on simple things like "Do I share these opportunities at all, with my allies, or with everyone?, in exchange for better relations, better influence, a bump to diplomatic relations, etcetera. By the same token from the other side you may hear "An Altairan diplomatic mission has introduced to us a rather interesting way of increasing our industrial efficiency, for which we are duly grateful, but it is worth noting that a number of our young, impressionable students appear to be considering Altairan Universities in the wake of this, ah, generous exchange of knowledge . . ."
3-C) Can ethical decisions be used to simply present special resource tiles on a planet, which would, in turn, actually implement the effect of the decision? I.E. if you get a "Good" Decision to set aside parkland for a morale bonus of +50%, rather than using it for industry for +25%, is there any good reason for doing that as a one time decision, rather than as a tile with a special 'parkland' unique building for it that would make use of the resource for the bonus? You could change the decision later, but you would never get the unique bonus again perhaps?
3-D) I've forgotten 3-D, and will surely post a post-script at noon tomorrow when I wake up going "THAT'S what it was!"
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I'm not sure how much of this is do-able, and I would appreciate feedback on both the ease of implementation and whether people think it's actually worth doing?
Thanks - Jonnan