There's a lot here to catch up on, (currently on pg 16), and way too much for me to attempt to respond intelligently to.
First up, I'm not that good a player in SP. I *am* challenged by 7 difficulty AI, often enough, with random moderates, and some source of automatic AIP over time. I tend to avoid Hard Spirecraft/Golems/Hybrid Hives. I almost always play with one homeworld, and I have some defense problems with my preferred extended empires. I play on normal ship cap, normal speed, full complexity. I tend to play longer games than I would like - I'm trying to improve my speed of play so games complete in a more reasonable time. I also don't play many games in a short time frame - instead playing over the course of weeks in fairly short sittings.
I am very strange, but I do not find myself blobbing all the time and I do not find myself taking the same knowledge choices. In fact, (in singleplayer 1 HW) I almost never find myself unlocking upgraded harvesters; it is rather weird how I almost always find the corner of the galaxy with the lowest possible number of resource asteroids.
On the blobbing front, I certainly do bring my fleet into a system as a big blob, and do often move it to certain targets as a big blob. However, with the special forces and improved guardians, I often do find myself splitting my forces up into three groups in-system. The fighters clear out the guardians for the sake of my starships, the frigates often stay near the wormhole out before later taking out the MLRS posts/spec ops posts because of their low speed, etc.
I still find Special Forces Patrols challenging and noteworthy after their new balance point. Something like 100+ Zombards, or Gravity Drains, or Tractor Platforms cause me problems - ones I can work through or prevent outright through elimination in other systems. I can eliminate them, I can work around them, they're good. I tend to use Mk2 Eco Command Stations, but due to map seeds, do not see the value of Harvester upgrades.
A suggestion: Try one Golemite AI and one random, Human Colony Rebellions, Zenith Miners, Spire Civilian Leaders, and (optional: Fallen Spire) on a simple/microcosm cluster map. Try to avoid getting any superweapons for as long as possible.
Tying champion nebulas to AIP floors does sound interesting. One thing I've been thinking about but haven't convinced myself of: Progressive Energy Tax. That is, diminishing returns on energy collectors (rationale: It's hard to build a "Smart Grid" in space). Just for example (but the numbers are not any final proposal): After five energy collectors, the next five offer 100,000 energy. After ten energy collectors, all the remaining ones offer 50,000 energy and no more and no less. Actually proposing this idea on the mantis would require me to actually think about the power cost per cap, and various other things.
As to ship unlocks, I often find myself forced by circumstances to take different paths. In my current game against the Golemite and Entrenched Homeworlder w/Spire Corvettes as my bonus and Fireflies/Infiltrators/Zombards showing up on the AI side, I've taken Plasma Siege Starships to help with the forcefields and boost the corvettes. I'm actually considering taking Etherjet Tractors as a bonus ship type as an attempt to deal with those Zombards - thanks to their sniper immunity the best I can do is grab campers on a wormhole with tractor riot ships and kidnap 'em. I'm taking Space Tanks over personal favorites in an attempt to handle Fortresses and Golems better (don't accidentally tick off an armored golem when you only have mark two fleetships and a few mark two starships). Spire Corvettes are currently outpacing the utility of the other starships thanks to the combination of their medium hull and shields that rebuild themselves eventually even outside of supply. They actually stay alive in this Zombard-rich environment. For once, I'm dealing with barely any pesky gravity or tractor units - For Now.
For games where the AI has lots of tractor units, I find myself favoring bomber starships. Gravity: sadly somewhat short range plasma siege starships or more missile frigates. Sometimes I find a reason for Zenith and Beam starships, but not for a few patches which have affected some things. I don't have a great spread of games to draw from.
Edit: Oh for everyone talking about economy nerfs, don't forget about the -other- extreme on the balance triangle: Eight players, 1 HW each. It's at least 160 AIP to get a second world for everyone, let alone three. I'm not saying anyone is wrong or right on this, merely I haven't seen any mention at all of co-op gameplay in economy discussion and it is significantly different from a multiple hw - one player game.