Then be afraid. It's in the game.
As others have pointed out, this aint moo2. For the record, moo3 had more stuff to fiddle with than moo2: it was a vastly more complicated game. It's just that it had so much stuff to fiddle with that it was easier just to let the AI viceroys play the game for you instead of microing stuff yourself. (and aside from that, there wasn't good feedback. You'd mess with a knob here and there, and the effects would be unpredicatble due to poor documentation and the complexity of the system).
Nod, maybe it's a dumb idea. I dunno.
Reducing clicks is an aspect of what I'd like to achieve. What I actually mean is I'd like to reduce the number of things that we have to display, and the number of things the player has to remember and fiddle with. Messing around with 3 combo boxes is ok for 10 planets, but what about 100?
As you said, one of the combos can be set and quickly forgotten, ie Primary Classification.
But secondary classification is quickly rendered moot in that hypothtical 100 planet game (or even in just a 25 planet game). That is to say, it's intended function (quickly re-adjusting your planet's output by minor amounts) doesn't seem valuable once you reach a certain number of planets. It's something I noticed while playing with my spreadsheet, trying to figure out numbers for the v.2 economy system.
If we marry secondary classification to the Industry of a planet, then changing a single secondary class can have real effects on the larger empire's stockpile of resources--espcially once we get facilities and technologies in the game that improve Industry. Further, it gives secondary class a "sunset clause". It's there when you need it in early game, then gets mostly superceeded by building stuffs in the mid game. Finally, it gives you some things to do with Industry that your otherwise not using.
As for changing industry to food: Cheetos. I rest my case.
Changing industry to research: SEMATECH. I use to work for them
. Basically, it's a fully functional semiconductor fab used entirely for research into how to make better semiconductors and fabs.
Please don't think of "Industrial Projects" as being something new: it's secondary class renamed and combined with v.1's Focus.