Another wonderful set of patch notes. The quality of these major updates continues to be awesome. It's quite amazing

About colonies: I think their profitability / return of investment is fine as it is, though I agree with nerfing Commerce. It is too much of a no-brainer in 0.95.
The biggest problem with colonies is that the game is currently too short to fully enjoy their monetary benefits. It takes time to survey planets to find good ones to develop, then it takes time for them to grow, then time to pay back the invested money. An experienced player will have already reached endgame by the time his colonies reach size 6, and at that point there is very little to spend all that money on. The solution to this is more end-game content / money sinks, which I'm sure we will see eventually

Are early colonies a good investment? Let's see. Pick a low-hazard world with farming and mining opportunities. These are the expenses you will want to make:
- ~100k for crew, supplies and other materials to colonize and build a comm relay
- ~100k to buy ships to transport the above (pair of nebula's and a freighter)
- 75k to build Farming
- 100k to build Mining
- 100k to build Waystation, so you can resupply at the colony.
- 250k to build an Orbital station, the most effective defense.
- 150k to build Ground Defenses, for the stability bonus.
- 300k for Patrol HQ, so you spawn some ships to deal with straggler pirate fleets, etc.
- 5k/month for an Administrator with Industrial Planning. Pays for itself so it's a no-brainer.
- 5-10k/month for Hazard Pay to grow to size 4.
Total: roughly 1.3 million credits all told.
How much money does this colony make? Depends on the quality of resources. Could be anything up to like 70k per month net profit. And that's after everything is build and colony population is at size 4, which could take over a cycle.
At 50k/month, the return of investment takes 26 months.
At 40k/month, it takes 32 months.
At 30k/month, it takes 43 months.
So altogether you're looking at 3-5 cycles before you see any actual profit. By that time an experienced player doing bounties will be lvl 15 and well into midgame. And that's just a basic colony. Further development with Megaport / Star Fortress / Military Base etc will cost millions more. So yeah, proper colonies are
not an early-game thing, and fully developing 3-4 colonies isn't even a mid-game thing.
That doesn't mean early colonization can never work though. You could settle a bare-bones colony with only a single industry and no other structures: just Farming, Mining or Tech Mining. And skip Hazard Pay. Then the investment is only 200-300k. It's not something you'd do on just any world, but on a world with good resources like a Terran with Bountiful Farmland or a world with Vast Ruins, it can be worth it. Doubly so if you happen to have Soil Nanites or a Mantle Bore.
Bottom line: fully developed colonies are definitely an endgame thing, but that endgame lacks money sinks so it's mostly for bragging rights. For the time being, colonies themselves
are the mid/late-game money sink. On the other hand, an early opportunistic colony can, under the right conditions, pay for itself and provide some benefit. So it's not like colonization is a completely wasted mechanic. I think it is fine.