Colony Pod
I didn't mess with this. The real problem I observe in AI play, is they stupidly blunder lots of Colony Pods into fungus and mindworms. And they don't make bases even when they could. Pods will just mill around instead. They also don't go on straight enough paths to destination sites. Decreasing the cost of colony pods may be a giveaway to the human player, but I'm doubting it'll change the AI performance much, because the AI already uses lots of them stupidly.
What might actually help AI expansion, is a Trance Colony Pod. However I don't think I'm willing to make this a free ability, and I'm not sure if the AI will us it if it costs more than a regular colony pod.
Former
I made them slightly cheaper.
Terraforming is the key to the game.
I dispute whether it's key to the
early game though. Although I'm known for my habit of planting Forests on Flat Arid / Moist terrain, a city with enough resource specials may not need any terraforming immediately. I've been experimenting with not obsessing about Formers immediately in such cases and doing other stuff.
Former is the best income source there is.
If you mean
energy, I'm not convinced that credits or research even matter all that much to winning the game. I've won an awful lot of games with low grade military units. Minerals I agree are important. Mines on minerals specials, forests, and enough food to make those squares workable, are the keys to victory. Whereas, it seems like if I get into the "build another lab / economy building" dance, the game just takes forever.
With that in mind I think this unit should cost 2-3 times more than early combat units to highlight its value.
Nope. In doing so you are designing a more
tedious game. That's not a virtue. The game takes long enough as is, and already goes in slow motion as is. You get more Formers sooner, the AI gets the same, so it's a wash.
Recently vonbach commented that the AIs in my mod terraform better, and I didn't have a good answer for why that would be. Now I am realizing, I made Formers cheaper for everyone a long time ago, and I'm used to playing the game with those. vonbach probably isn't and so he may be seeing the difference. The only other thing I've done recently is make a Rover Former predefined unit. The AI does build some of those, and that probably does help, because they're quicker at laying roads. But the AI doesn't build a lot of them, so it's probably not a big impact.
Transport Foil
I made the Foil and Cruiser chasses cost half as much as in the stock game. They are now comparable in cost to Speeders and Hovertanks respectively. Again this is the philosophy of the faster game, with everyone in the same boat (pun intended). I have noticed that sea base combat becomes an "easy come, easy go" affair. Yes I may spam out a lot of ships to take a lot of bases, but then the enemy does the same thing and takes them right back.
First, they are excellent mean of scooping sea pods and harvesting artifacts early on which makes them quite valuable. I consider this a human exploit as AI doesn't focus on this strategy.
The real answer to that problem, is to have the human play with no supply pods except at starting locations. I played that way for about a year, on very large maps. Nowadays I don't care.
Supply Transport
Other people before me said many words about Supply Transport abuse and how cheap it is comparing to its benefit.
Ocean minerals are not worth anything. Even if you spend a lot of time building mines on top of minerals resource specials, they only yield 4, the same as any Rocky terrain on land. There's usually tons of Rocky terrain on land, much closer than the uncommon Ocean minerals special. You will wear yourself out pushing Supply Transports around trying to get to the things. If a player wants to torture themselves with this kind of marginal gain, I say let 'em.
Costs within the game aren't the only cost to consider. Real world costs of the player's
time and aggravation should be considered. I call this "the mouseclick budget". Too many of those, and the human player falls asleep! Whereas the AI never gets tired and will do the most tedious things over and over again.
Pricing it higher would be an easy fix to put it in line with other recourse multiplying facilities.
I just put them later in the tech tree. For awhile I had them too late, to the point of ridiculous. Now they come "midgame to late midgame". I don't have a problem with a player gaining an advantage by which they can win the game, once they've done
a lot of stuff to put themselves in a position to win. If the player has exerted themself sufficiently, let them go ahead and win. In the real world, the mopping up operations are going to take several more hours anyways. This game has
way too much waiting around and tedium in it.
Even at this price it is still very lucrative investment as it brings raw minerals those further can be multiplied by mineral multiplying facilities.
Have fun with the Global Warming floods and mindworm apocalypses. Feel free to let the children have power tools to cut their own fingers off with.
Probe Team
This is pretty useful war helping unit that is not intended to die pretty often.
I dunno, I don't train 'em, because I can't really afford to put a Command Center in every city. Got other things to do. Military units get made in Command Centers, probe teams usually don't because that's where I've got the spare capacity to make them. Probe teams often die anyways even when they are trained, so as far as I'm concerned, they're disposable. If I get a free tech from a probe team, that's a good trade.
In my mod I eliminated the +2 PROBE benefit of Fundamentalist. The Data Angels are the only faction that get a PROBE bonus, and I'm about to eliminate the University's PROBE penalty as well. Basically I've nerfed them. I've found the AI's propensity to spam them to be very, very obnoxious. This misfeature has caused the single largest number of rage quits over the years. In my mod, they're down to a dull roar now, because the AI doesn't perceive them as being the world's most ultimate advantage.
Scout Patrol
That's a
combat unit. Particularly in my mod where you can't get armor until Tier 2, and can't get a weapon (in my version 1.26 under test) until Tier 3. Scouts get +25% against enemy bases because they're an infantry unit. Yes I'm having a lot of Scout vs. Scout fights lately. It was a thing in Civ IV as well, storming the enemy with the Aztec's early Jaguar 1-1-2 unit.
I'm evolving towards every time a new ability is granted, a new Whatever Scout predefined unit is made available as well. Currently I'm testing Marine Scouts and Cloaked Scouts. Trance Scouts are already field proven for a long time now; the Aliens start with those. I've got Light Artillery as well. They don't do much damage, but they do enough against
Scouts to have some value, and they can tear up terrain improvements. Gotta knock out those +50% defense Sensor Arrays somehow.
Two consideration here. First, as with Transport Foil this is a mean of quickly popping a lot of land pods with goodies and artifacts. The ROI is too much for 10 minerals cost unit.
They're bloody slow. Are you sure you want people to actually play this game?? You seem to be looking for ways to penalize very basic gameplay like there's some big problem with it. Knocking out Scouts is not a free lunch, they cost Support. Scouts get killed by mindworms. There's no problem here,
please move along, nothing to see. Go home folks...
AI pops pods as well but it doesn't spawn swarm of cheap units to swipe the land clean as fast as possible.
So again, play without pods in your game if it bugs you so much. Rather than trying to uproot very basic game mechanics around this issue.
Second, Scout Patrol with Hypnotic Trance is a basic base protector unit used at 95% of your bases.
What's wrong with defending against mindworms? Not like they're any good against any other weapons. They're not even good against
other Scouts, as attacking Scouts have the +25% advantage against a base. Well, better trained Scouts do fine against worse trained Scouts, and that's how it should be. Anyways, going on about the mindworms, you sound like some kind of Nature Loony!

Sea bases are designed to be rich in nutrients and energy and poor on minerals.
With the notable exception of the Pirates, whose +1 minerals on water is the biggest free lunch in the game. That's why they're now my "sit back, relax, and do nothing" faction. They don't need to fight anybody!
With that in mind I don't see a single reason why sea base units should cost any different than their land counterparts.
Because I made Foil and Cruiser chasses costs cheaper, sea colonies are also cheaper. They do produce more quickly. Playing in the water is far less of a drag now. The Pirates aren't the only faction that benefits from this. The Alien factions seem to have AI that believes in water bases. Also any faction that has a small island start, can go oceanic. I've minimized the potential of small island starts with better map generator settings, but it can still happen.