I completely agree with (about) everything you say. The problems you mention with Planetfall however are I believe not a shortcoming in design, but me not yet having the tools to implement the intended design. They require SDK changes, which I cannot do.
I generally find it so very much to my advantage to get a boat in the water as soon as I can, to collect all the sea pods and collect prizes ranging from bonus credits to more sea units with which to scout out Planet's oceans. And the AI don't seem to take advantage of this at all. This leaves me with the circumnavigation bonus, a lot of extra energy credits, and a dozen or so gunships and transports. If using the unity supply, this can be done before researching Doctrine: Flexibility.
A possible balancing solution seems obvious: let more IoDs spawn, so foils can pop less unity pods before getting wacked.
Problem with more IoDs is however that in the early game sea terrain improvements would quickly get pillaged, making building and using aquaformers pointless. Therefore I think there should be a Flowering Counter level (say 25 or 30) under which native life cannot move into factional borders, giving players some breathing room in the start.
Until that is available, I'm wary of increasing native life spawn rates.
I've also found farms so essential that I build them wherever I can, because now they increase in power as they're used. I can get ridiculous amounts of food from what they grow into, so I may quickly build formers and mind worms, or alternatively get more people, particularly specialists. I rather think the creators of normal Civ4 had a better idea with the growing terrain feature going to something that improves monetary wealth.
Farms currently aren't working as intended. I'd like them to have two downsides to balance the immense value of farms:
1) Farms give a Planet penalty to the base that's working the tile. The improvements the farm upgrades to get bigger penalties. Unfortunately the XML tag which should do this, isn't working.
2) The speed of farms upgrading should depend on the Flowering Counter. The lower the Counter, the faster they upgrade. If the Counter is above 50, Farms wouldn't upgrade at all, except for Terraformers - that civic gives +100% upgrade speed. As keeping the Counter low should be somewhat of an uphill battle, it would take effort to reap the full rewards of farms.
At areas of land where I can't build farms, I instead generally litter the terrain with hybrid forests. They give +1 each of nutrients, minerals, and energy from the start, while greenhouses and normal forests tend to be missing one of these. I can also then increase the food content with tree farms. So, yeah... not a whole lot of strategic thought there.
I'll limit planting Hybrid Forests to the Hybrid Ecology civic. Under the Terraformed civic they automatically turn back into normal forests, but I guess that process goes too slowly. (And under the Enclosed Biosphere civic you can't build them at all.)
I don't know whether I'm missing something (I doubt it), but it's also getting me to question the usefulness of the Enclosed civic (for which I still think the gameplay description is too complicated). A lot of terrain features suddenly stop producing food, and greenhouses at up to two nutrients each don't produce the surplus necessary to promote specialists. I always end up not bothering with it at all and beelining to Centauri Meditation for the Hybrid civic instead. (Due to my tendency to want to found the Voice of Planet religion and build hybrid forests, I generally want that tech early anyway.)
Again a case of not yet having the required tools. Instead of that long list of food penalties, I'd instead prefer to let the Enclosed Biosphere civic give +1 nutrient on Flat Arid and Flat Polar terrain.
I had a game though where I started on a peninsula cut off from the main continent by some Peaks. So instead I turned to the water and switched to the Enclosed Biosphere civic. The civic gives +1 energy to windmills, so together with Kelp Farms that gave me 3-0-2 on Shelfs. It was awesome! (Well, until a barbarian army of IoDs I was unprepared for suddenly appeared and pillaged all the windmills in sight

)
After hearing the mention of how the Enclosed civic is supposed to promote the use of specialists and greenhouses, I do have an idea of what that civic could say...
+2 food per specialist, +4 food per greenhouse, -50% food total.
So specialists would consume (2-2/2)=1 nutrient each instead of 2, the greenhouses would provide a surplus of (6/2-2)=1 nutrient each instead of 0, and the nutrient output of other stuff would basically drop. If this civic still doesn't provide worthwhile against hybrid or baseline, it may have to also gain +1 free specialist.
Sounds even more complicated than what's currently implemented.

+1 food for specialists sounds interesting though.
For the record, what I was thinking of to create a synergy between enclosed biosphere and specialists involves crawlers. These units would be able to create robotic variants of certain terrain improvements like greenhouses, mines and windmills (but not farms, forests or condensers which can't be built anyway under enclosed biosphere). Working these robotic terrain improvements would give a free specialist in the working base.
Unfortunately there is no tag yet which only gives a free specialist when the plot is worked. And giving the free specialist even when the plot isn't worked would be overpowered. So I'm holding off with implementing this.
Zakharov, Santiago, Lal, and Deidre all asked to become my vassals during peacetime, and I accepted all of their offers. A few turns after I built the Planetary Council Headquarters, I found that I had so many votes from myself and my vassals that they exceeded the amount needed to win diplomatic victory. I decided to give it a try. And sure enough, I won the game a few turns later. As for why four faction leaders asked to become vassals, my guess is they saw that I was high on the power chart (likely due to my fleet) and decided to seek protection.
I had that too once. The reason is probably that <VassalRefuseAttitudeThreshold> is set to NONE for all leaders. Call it laziness when updating Planetfall from vanilla to BtS. Setting the tag to ATTITUDE_PLEASED or something should fix this I think.
Btw, if you want to help with Planetfall despite not being able to do SDK yet, this is a possibility: figuring out fitting diplomacy values for the leaderheads. Currentl they're all copies of Washington.
I was half way across the tech tree and only with gatling lasers, but apparently, Miriam didn't even bother with anything beyond pulse units
Unfortunately, the AI doesn't use the workshop, and doesn't use anything but the most basic weapons.
Because of this I'm planning to switch to a non-workshop unit system instead, but it requires some new XML tags in PromotionInfos to work properly. An SDK matter.
(using a network node to make a citizen into a librarian)
Yeah I too find Librarians useless. But that's because I find the BtS espionage system in general boring and useless. I have some vague ideas to improve it, but it's low priority considering all the other things that require attention.
Yeah, I realize I should be a lot more appreciative than this.
Well, your experiences are appreciated, and I agree with about everything you say. It's just that this mod is still very much a work in progress, so don't yet have too high expectations of it.
Anyway, perhaps upping your difficulty level to Emperor or something could still provide some challenge/fun for you in the meantime?