I've been engaging with colonies in 0.95 for a bit now, and colonies are in a really good place balance wise, provided the player does not build commerce. While the new items generally equalize the playing field when it comes to economic power (read: Income), commerce is a single, very obvious outlier. I have not seen many screenshots of colonies without it, and it's not because of the open market feature.
Multiplying income by +50%, another +50% from the item, +25% from an alpha core and +25% from each improvement is brutal and causes the building to actively diminish choice, rather than add to the option pool.
It is always, without fail, the most optimal choice for the second colony slot. Anyone building something else only does so because they haven't given it any thought or, like me, actively avoid optimization. Sadly, if given the option, players will optimize the fun out of the game, and commerce enables this to a very high degree.
It needs a nerf. The stability reduction is not enough of a drawback - it's easily rectified (the mandatory defences, patrol HQ and Star Fortress, give you 8 stab with commerce, without any other upgrades).
I had the exact same problem with the Privateer Base, which was just too powerful to be "optional", and became "must-have". Spent a good while trying to figure that one out, and finally settled on the two colony slots solution.
Making it take two colony slots would make the industry only effective on planets with good conditions, or high base income, and also prohibit building it until 2 slots open up, which is a very high initial investment and an interesting, deliberate choice that has to be taken by the player.
Honestly, in my personal opinion, it'd need the 2-slot requirement and a reduction in base effectiveness to 25%, 25% for the item, 25% for the alpha core, and 10% per SP, to be in line with the other industries.