It gives +25% more income (+50% with alpha core) at the cost of -3 stability.
Honestly, with -3 stability, unless there are more ways to boost stability, I do not see using this unless the colony is size 10 and all of core worlds are dead (no income from exports).
Currently, with Free Port, the most stability the player can stockpile (if he has maximum colonies), without using cores and with makeshift comm relay, is 13, and that is with maximum colony skill investment (since admins cannot have all three skills like player and faction leaders). Without Planetary Operations, 11. If player uses alpha core as admin, then that colony gains permanent Pather cells for -1 stability, which probably maxes out the total at 12.
Free Port is a must by late-game if I want to grow the colony faster (and I do if it takes five in-game years to grow from 7 to 8 ). Yes, the -3 stability (plus more expedition spam) hurts, but the benefits from higher growth, and higher profit from boosted accessibility and illegal commodities is worth it.
However, there is no way I can take -6 stability unless I max out colony skills and barely eek out 10 stability. (Alpha cores will probably max at 9 thanks to Pather cells.) Of course, this assumes getting max colony skills (if they stay the same) are worthwhile next release. If they are tier 5 skills, I may not want to get those if it means killing off the fun combat stuff. (I wish colony skills were tier 1 like Navigation/Sensors, colony skills are up there in importance.)
Stability is a top-tier stat. I know Alex mentioned that he may reduce impact on income, but it if still reduces some income (along with other debuffs) from less-than 10 stability, then Commerce will still be a trap.
Free Port will give more income, more population, and does not cost an industry slot.
New Commerce as an industry will be a worse trap than current one. At least current one did not cost anything beyond industry slot (and more clicks to access ship storage). This one will be worse than useless if the colony needs Free Port to grow and player cannot maintain 10 stability after taking another -3 penalty from new Commerce.
P.S. For smaller colonies with two industries, I see building only Military Base (for defense) and either Tech Mining or some Industry to meet demand for something. Later when colony has three industries, it is big enough to need Free Port (until size 10, but that takes too long), and cannot take anymore stability penalties unless my character was built for colonies.