Commerce being very good to nearly must-have is enough of a penalty, especially with -3 stability. Military Base being required for every planet (at least in games where player cannot colonize all planets in one system) is bad enough. I want to have or need some variety in my colonies to meet demands.
Dealmaker Holosuite may be good, but if I am avoiding Pather cells, I would only use it if I have no other item needs (like nanoforge), since most items add +4 to Pather interest (and it takes +7 to spawn a cell). Two planets will be dedicated to heavy industry and fuel production, no dealmaker on those worlds. Of course, that assumes dealmaker can be found. In my game, I found other items instead, and I would need to grind the historian to conjure up those dealmakers.
Commerce's income boosting is most useful after player nukes the core worlds and kill all income from exports. At that point, other industries is for self-sufficiency reasons (i.e., meet demands).
Commerce? Always best second choice? ...What are you putting as your first?
Because for me, the first choice is heavy industry, and the second choice is refining; that typically gives more profit than commerce would because heavy industry really isn't a profit-generator, and more importantly, it makes my heavy industry immune to trade disruptions. Commerce comes third at best - and generally by that point I'm no longer struggling to keep the colony supported and don't particularly care to add another -3 stability on top of free port. (Now, once the colony hits max size and I can turn freeport and hazard pay off... well, that's also frequently the point where I'm suddenly making enough credits that I don't even care about commerce.)
Now, for a one-off "I'm building mining on this gas giant" sort of colony, yeah, commerce comes second. But that's because there simply isn't anything else that's really worth building there, not because commerce is overpowered.
For me, Commerce is usually my fourth industry. First industry varies by planet, but usually one among Farming, Mining, or Heavy Industry, depending on planet. Second industry is usually Military Base. Third industry is another commodity producer. (Occasionally, second and third choices are reversed.) Fourth is Commerce.
Oh, as for Heavy Industry and Refinery, I would only do that if I do not have Mining on it. Heavy Industry with forge is +4 interest, and Refinery alone is +2, for +6. If I add Mining, that is another +1 for +7 total and hello Pather cells!
