Should we have a "universal" theme for the technologies we want everyone to be able to get, maybe primarily for things like governments, policies, sensor techs, supply boosts (assuming they aren't all rolled into policies), planetary defenses, and the like?
While this may be necessary in specific cases considering current mechanics, I generally don't like this as it implies that there are mandatory techs that everyone needs to have access to in certain situations. This again implies that the underlying mechanic is binary. For example, take current stealth mechanics vs empire detection strength. It is an extremely awkward design. On the other hand, it isn't necessary to have access to the best weapons in each theme: You can balance it against having better armor and/or shields in the other themes.
If you were to remove the binary nature of stealth, it would not be necessary that every single theme overcomes the maximum possible stealth level. Say, for example, there are different levels of vision (arbitrary thresholds)
1) Detection > stealth -> Full vision
2) Detection > .75*stealth -> Full vision on map but stealthed ship still gets first strike bonus in combat
3) Detection > .5*stealth -> Vision of fleet on map; no ship info
4) Detection > .25*stealth -> Vision of fleet on map but only if moving; no ship info
5) Detection < .25*stealth -> No vision at all
In this case, it may be perfectly fine that one theme at endgame has only 50% detection of maximum possible stealth levels: It has the ability to counterplay and may have stronger ships to compensate. Still, the arms race is encouraged and both sides gain something from pushing their detection/stealth. Probably also should have partial stealth bonus when Detection > stealth to encourage actually going for stealth with more than the stealthiest theme but you get the gist.
Overall, I think different themes should tackle the same problems in different ways. You already discussed expanding on poor/hostile planets in another thread. For another example, take supply :
i) Emphasize stockpile and fuel rather than supply
ii) Provide straight out supply bonuses to your colonies
iii) Provide a building with relatively high cost which offers a large bonus (but allow some later passive tech to override that effect to avoid lategame spam)
iv) Decent supply boost but only on outposts, not on colonies.
v) Require and strengthen logistics focus
vi) No "good" early supply tech. May or may not adopt early policy which provides supply but at nontrivial cost.
For detection, there also are several approaches: Empire meter, reducing stealth of enemy fleets nearby our planets, use ship parts instead (meh, micromanagement), rely on espionage to find enemy fleets,...
With redundancy across themes we should probably make any techs that provide boosts not stack across themes, so that say choosing two themes is a guaranteed way to raise your planetary defenses so that you cannot get invaded or sensors that can beat anyone's stealth?
More elegant approaches than straight out non-stacking could be at least in some places
1) Boosts with contradicting conditions (e.g. biotech boosts population on poor/hostile planets but that is incompatible with terraforming)
2) Use a policy where it makes sense and the boosts are of comparable strength
3) Make stacking unlikely or require dedication by putting synergy boosts in mid to lategame tiers. Yes, you may take that biotech T4 which boosts population on good environments AND get terraforming from mechanical T4. That may actually be a viable strategy but it will either come late or significantly delay your progress to high tier techs in either branch.
I don't know if I can make their weaponry and Energy's distinctive enough.
My opinion: Embrace overlaps between themes and use it as a possible gateway to hybrid strategies. Say, both crystal and energy physics get lasers as first weapon choice and will each get different weapons later on. Instead of going deep in one theme and replacing the early game laser, you could pick the refinements for the laser from both themes, e.g. one theme focuses on rep rate of pulsed lasers (i.e. more shots), the other one improves pulse energy (i.e. damage/shot). Add stacking shield bonuses to compensate for missing out on later hulls and at least part of a viable hybrid strategy is born. Balance concerns? Not much. If it is too strong, it can easily be nerfed by not letting some of the problematic techs stack. If too weak, who cares. It's another possible fun build which may or may not be buffed eventually.
To me, there are obvious fluff connections between crystalline <-> energy <-> mechanics <-> cybernetics <-> biotech <-> crystalline, might as well make use of them.
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