My Crusade 2.31 balance issues

I agree with these from your original post (made a few small edits to some of your points):

Other things that I think are unbalanced:

- As mentioned by tetleytea, some of the resource types can be very rare, while others are usually all over the place. Antimatter is necessary for so many things (all missile tech, some engine tech, Antimatter Reactor (or whatever that prod-boosting building is called), etc). If you happen to not be located near a black hole, then your race is at a severe disadvantage. If you start a game with black holes set to rare or none, then there is no way to get any Antimatter (is there?). This could be a fun game mechanic, but Antimatter seems to be a problem material most of the time, while the other resource types usually aren't. Some of the special resources (like Snuggler Colony) seem to be mostly useless.

- Trade Routes aren't valuable enough. I think they should scale more than they currently do based on the "age" value.

- Trade Routes are invulnerable to being disrupted. We don't necessarily need to be able to shoot the little freighter (which I think was a thing in Galciv II). I sort of expected there to be an option to put a ship/fleet in "Guard" mode on an enemy trade route "line" on the map and disrupt it or something.

- Component size is just weird. Shouldn't the engines/thrusters/life support on a tiny ship scale WAY down compared to a medium or large ship? Something the size of a fighter should be able to fit INSIDE one of the engines that powers a medium or large ship. Weapons and most other components shouldn't scale at all (and I think that already works as it should).

That completely depends on your galaxy setup.

Two of the last several galaxies i played in had ridiculous levels of antimatter. So when you have antimatter, you make antimatter-aid. If your map has none, you don't.

I agree with most of the points, in particular:

-  That I can build a single, blazing-fast transport, load it down with Prototype hyperdrives, and own the game.  They don't destruct when you invade (and win the invasion). 

-  Planetary invasion completely imbalanced.

-  Planetary defenses useless.  You don't get invaded.  Offense gets too many advantages.  

I made a suggestion about it in the ideas forum, right now it's too easy to roll over the AI's planets. (In short : I think there should be a turn for the invasion intitiation, and overall speed should be toned down)

Citizens can be super powerfull, I think the ai can't use their potential. (Epiphany can be a killer since the tree is linear, easy to run to doomray when the time has come.. better to use the conquered scientist citizens for the task). 

Ai tends to flood the map with single ships which are no threat at all

resources should scale with galaxy size/number of players.. maybe they do, I'm not sure. In my huge galaxy/16 player gamewe had plenty of everything (in my game promethion was like trash.. since I used almost only beam weapons)

Agree with the vast majority of this post. The move-5 prototype hyperdrive seems ridiculously OP and I assume it has to be a bug?

I would add a few more things:
1) Ship defenses are very poorly balanced. A Barrier Field Generator is lower tech than an Invulnerability Field, it has a much lower build cost and only slightly higher mass... yet the BFG gives +20 shields to the entire fleet, while the IF gives +8 shields to a single ship... and you can stack multiple BFGs to give very large + bonuses to an entire fleet. The same is true for Point Defense Arrays versus Aereon Missile Defenses. There is absolutely no reason to ever get the single-ship version of the defense.

2) Defenses are made even worse by the high strength of defense-piercing modules. Sure, you can stack BFGs to get 250 shields per ship on an entire fleet... but your opponent just needs Shield Punch and Leaching Field to almost completely negate those shields.

3) The ease of overcoming defenses means that there's no incentive to diversify your weapons. Once you start researching beams, unless you run out of elerium (unlikely) you can just keep making beams. If enemies stack a ton of shields you put a shield punch on and keep on building doomrays.

4) The Governance tech tree seems rather overpowered for its cost. The research point cost doesn't seem to scale much going from Interstellar Governance on up through Star Federation (unlike some tier-3 military and engineering techs that are stupidly expensive) and yet it it gives big +% bonuses to Raw Production on all of your worlds. No matter what your build order is, going for Governance techs early on seems to be the correct strategy.

5) Starbase Interceptor Drones sound like they'd help keep your starbases alive against late-game large/huge ships. But they are completely useless because the drones start out 20 miles away from the starbase. All of the drones get killed long before the starbase can fire upon an enemy.

6) In fact, Starbases are just way too fragile in the mid to late game. It costs over $6,000 to upgrade a new starbase to fully maxed defenses, but it'll still lose to a single Large ship with tier-3 weapons. You might as well not bother.

7) Speaking of starbases...it seems strange to me that the first player to put a Mining Starbase near a resource gains unbreakable control over the resource until that starbase is destroyed. That makes cultural builds and cultural starbases a lot less powerful. You could have enough influence to take over asteroid mines, space hexes, and even entire planets... but that darn starbase and its darn antimatter mine will remain enemy-controlled until you declare war. That is pretty awful if you're trying to be peaceful. (which is hard enough in GC3)

Another thing I thought was balanced right:

The Snathi campaign.  Man, I got defeated a lot on that one, until I figured it out. 

New balance issue:

The diplomatic penalty for Espionage looks too high.   Getting diplomatic minuses from EVERYBODY for "You know what you did" simply because I took my one free spy and spied on one race is a bit much.    Espionage's usefulness is already on the fringe as it is; so incurring penalties to something as core as diplomacy is enough to make one simply not want to do espionage, or pick the Onyx.   Espionage is a cool, fun feature:  you get to see what the AI is doing.    Now, if I got caught trying to sabotage a race I was not at war with, I would reasonably expect to take a diplomatic hit to them and their allies.   But not from just parking one spy on somebody, and not a hit to everybody.

Does this statement in the diplomacy screen mean that I was caught spying?

That was NOT obvious at all. It seems that it was meant to be funny, but I've been trying to figure out "what I did" for a while now. This message should probably be less cutesy and more descriptive.

In my experience, I get "You know what you did" diplomacy hits the minute I spy on somebody.  Anybody--does not have to be that civilization.

-The nearly pointless population, combined with synthetic races needing to build it instead of building propaganda & such is particularly problematic.

I think that the problem with factories is related to the near useless population