Genejack Factories...when to use them?

[Kirov]

That still won't let you run 60 minerals in a base under FM; with a mod I'm working on, that will be possible with Green.  Though just for support it will work, unless the enemy identifies that base (not hard, I think enemy units show their home base) and spends what is needed to take it.

I never asked - how exactly are you planning to change things that are firmly hard-coded?

Second thing - are you sure you're taking into account all indirect results of your changes? Like the fact that you give mineral boost to Deirdre, already a very strong faction, and you make Believers weaker, already a shunned faction? That you can make Manifold Nexus on par with Monsoon Jungle? What about Tree Farms and other ecological facs, will they matter less or more?

[Yitzi]

I never asked - how exactly are you planning to change things that are firmly hard-coded?

That's why the mod isn't done yet (and probably won't be for a while); I'll need to make a scient-style patch to un-hard-code them before I can make the mod itself, and since scient isn't available that means I need to figure out on my own how to do that.

Second thing - are you sure you're taking into account all indirect results of your changes? Like the fact that you give mineral boost to Deirdre, already a very strong faction

I've heard that Deirdre is strong, but I've also heard (from a different source, of course) that she's very weak due to inability to run Free Market.
Furthermore, note that her current strengths lie largely with energy focus (the high efficiency), whereas the new strengths will favor mineral focus, so it's difficult to get full benefit from both.
In addition, it really only gives her a mineral boost when she runs Planned; with Green anybody can get minimum ecodamage, and she can't run Free Market.  And running Planned negates her other big advantage.  So the end results of major strengths and weaknesses are:
Strengths:
-Can get good growth via Planned with less sacrifice of mineral/energy than most.
-Good native hybrid faction.  (Dawn is better for native momentum.)
-Fairly good balance of minerals and energy.
Weaknesses:
-Unable to get as much out of energy focus as most factions.
-Poor momentum play when not going native (due to -1 morale).

The result is a fairly balanced faction which can do pretty well at anything, but can't keep up with a faction that plays fully to its strengths.

In terms of strengthening factions, the real beneficiaries are probably Cha Dawn and Yang, since they tend not to be good at energy focus anyway.

and you make Believers weaker, already a shunned faction?

Believers really don't take that much of a hit.  -1 PLANET translates to +33% ecodamage when running Planned or Simple, +100% when running Green, and absolutely nothing when running FM.  So the Believers might not want Green as much as many, and will have more ecodamage than most.  Note, however, that if the Believers are on a war footing (the case where they do best anyway), they can have more minerals and just put some of their very high free support into extra fungicidal formers and empath/trance scouts to deal with the consququences of ecodamage.  (As for global warming, that often hurts their enemies more than them.) 
While my planned mod will mean that it starts to get uncomfortable (around 2 ecodamage per base) around min/base (improvements are more significant as compared to minerals by a factor of 5) equal to 1200/[techsX(3-PLANET)] (assuming centauri preserves, thinker or transcend difficulty, average native life, no perihelion), you're not going to have serious problems (around 10 ecodamage per base) until perhaps 5 times as much, which is fairly difficult to reach even for Believers not going Green.  Of course, with Market and a lot of techs, even 5 times as much might be only in the low 30s, which means that mineral focus under market is just begging for trouble.
Keep in mind...under the current system, the clean mineral soft cap is actually fairly hard, even running Green.  With my mod, the cap running FM will be almost twice as soft as it is now running Green.  And of course it places a limit on how much mineral focus you can do, but you don't lose the other FOP (well, except in that it forces you to cut back on the boreholes until Hybrid Forests, which I'm planning to move to the late game), you just have to put those FOP in other things.

The real hits are probably Domai, since he can't run Green, and Roze, since she'll want to run FM almost always anyway.

But why are Believers shunned?  They're actually fairly good as a momentum faction.  And running power/fundamentalist with command centers, their troops are only a monolith away from 187.5% attack effectiveness, making for an extremely nasty war machine (especially since with that setting they can maintain a huge army fairly easily).
Maybe it would help if you'd list the perceived strength of each faction, and why they're strong or weak.  I know that aliens and cyborgs are very powerful, and Cha Dawn is generally considered to be fairly weak, but other than that I don't really know that much.

That you can make Manifold Nexus on par with Monsoon Jungle?

Should it not be?  They're both landmarks, why should some landmarks be more or less effective than others?  (Note, however, that I am also planning to make pop booms harder, which will of course weaken the Monsoon Jungle somewhat; the Manifold Nexus probably won't be on par with the old Jungle unless your empire is really big.)

What about Tree Farms and other ecological facs, will they matter less or more?

Less in a large empire, because they won't boost clean minerals, but more in a small empire because there will be more minerals to be halved.  (Tree Farms are worthwhile anyway, for the economy and psych bonus.  Centauri preserve will be worth it for mineral-focus factions, not so much for energy-focus.)

[Kirov]

It would take me a long time to describe pros and cons of each faction, so maybe another time, but I'm afraid they're far from balanced. The top three factions are Uni, Domai and Hive, and it's not just my opinion. Uni for techs, Domai and Hive because the INDUSTRY SE choice is widely considered to be the most important one in the game. If you give any kind of boost to Yang or Domai, you do the opposite of balancing.

I can list the factions in my personal order of strength, but it's really subjective the lower it gets. Particularly Sparta and Believers can be stronger in skilled hands, they're simply not really my style. This breakdown works for me, though.

Tier 1: Uni, Domai, Hive
Tier 2: Aki, Morgan, Deirdre
Tier 3: PK, Data Angels, Sparta, Believers
Tier 4: Pirates, Cult

I don't count Aliens, because nobody counts them. They're strong and unbalanced for MP games.

[Yitzi]

It would take me a long time to describe pros and cons of each faction, so maybe another time, but I'm afraid they're far from balanced. The top three factions are Uni, Domai and Hive, and it's not just my opinion. Uni for techs, Domai and Hive because the INDUSTRY SE choice is widely considered to be the most important one in the game. If you give any kind of boost to Yang or Domai, you do the opposite of balancing.

Well, I am planning to weaken the importance of tech slightly, so that will help with Uni (as will the fact that while it will technically be able to be able to pop boom, it will find it extremely hard.)  As for the importance of INDUSTRY...making production capability a mix of INDUSTRY and PLANET should help a lot on that count (especially with Domai, since he can't get positive PLANET until late game).  Discouraging the "lots of small bases" strategy for any but committed momentum players will also help, as INDUSTRY becomes less important when you don't need to build facilities in as many bases (units and formers are useful, of course, but for units MORALE can be more important than INDUSTRY unless you're going pure-defense, and pure-defense is highly vulnerable to attrition, and as for formers, after a point you start facing diminishing returns, especially before Clean Reactor becomes available.)  And of course I plan to weaken crawlers heavily (I'm thinking raising the module cost from 8 to 45, and saying you can't crawl boreholes until Industrial Nanorobotics), which will of course reduce the importance of INDUSTRY quite a lot.

I can list the factions in my personal order of strength, but it's really subjective the lower it gets. Particularly Sparta and Believers can be stronger in skilled hands, they're simply not really my style. This breakdown works for me, though.

Tier 1: Uni, Domai, Hive
Tier 2: Aki, Morgan, Deirdre
Tier 3: PK, Data Angels, Sparta, Believers
Tier 4: Pirates, Cult

I don't count Aliens, because nobody counts them. They're strong and unbalanced for MP games.

I actually have an idea for balancing them.  The real brilliance of it (if it's ok for me to be that conceited) is that it uses the aliens' own strength as one of its major contributors, meaning that it can't make them too weak.  (The idea is simply to say that aliens cannot take part in an allied victory.  Thus, instead of being the factions everyone wants to ally with for an easy win, they're the factions everyone sees as a threat, and a major threat due to being so powerful, so coalitions will be formed to keep them down...until they're weakened enough that the threat can't sustain the coalition.)
And of course nerfing recycling tanks (an essential part of the anti-small-bases mod) will help reduce the power of aliens as well.