Am I the only one that thinks that researching with factories or building with labs is crazy!?
Of course not! Though crazy is not the word I'd use...
I don't mean it is a bad strategy;
I wouldn't call that a strategy, but rather (ab)using poor design.
in fact it is a good way to boost your production if you can keep from going broke.
One that goes against what in any other game would be called an undisputable rule (labs research, factories build).
such as the map scale is way off
Every scale in the game is way off. Not only the spatial scale as you mentioned, but also temporal scales (going from imperium to republic to democracy to federation in a few years for example; taxes every week); size scales (the hulls' sizes, tonnages, etc; components' sizes; special modules about the size of early weapons; fighters that don't feel like fighters); cost scales (components' costs, projects' costs, etc); and miscellaneous scales (people eat 1 kg of food per week

); etc.
It would be more intuitive to replace the current 4 sliders (spending, military, social, and research) with 3 sliders (factory output, military/social factory output split, and research output).
That would be one way to go. Spending doesn't make any sense whatsoever.
It is but one of a list of several things that are crazy
Actually, I think it'd be a lot easier to list what is *not* crazy in this game
I'm sure there are more....
Like blank hulls have integrated (latest model) drives (which can cost more than the hull itself), plus Sensors and Life Support?
Initially civs have one ship for which they don't (and won't any time soon) have the techs for - the flagship.
The UP both exists and doesn't exist while you don't meet any/all races.
Tourism income (as tourism) doesn't make any sense.
The Universal Translator has to be researched, even though you're part of the UP already, and can even do stuff without it.
You can't colonize special environment planets you don't have the tech for, but you can invade them.
Population growth and tax income being some strange functions.
Sizemods.
A load of doubling effects, like miniaturization/research, farms/PQ caps, techs/bonuses.
You don't actually need starports for some actions which you should.
An Orbital Terraformer that besides occupying a tile works for *all* planets.
Peacekeepers that aren't really peacekeepers, Pirates that aren't really pirates.
Population in flipped planets that converts automatically to your own race (including soldiering bonus).
Sensors and Life Support modules are cumulative.
Orbital Construction that requires ships to be launched.
The way trade routes work.
Almost all of the invasion tactics, really out there!
Some races start with Ion Drive.
It's 2226 but you start with almost a clean slate (the background story doesn't make any sense either, the game follows part of it but contradicts most of it).
You start with a cargo hull (which just got much less useful now) even though according to the techtree you don't have the knowledge to put hulls bigger than small through a warp field.
You start with your homeworld almost empty, but you already have 3 ships in orbit, and once colonization starts you develop planets quite fast.
Rush buying items, from anywhere in the galaxy, any item, whatever race, always from the same corporations (earth corps at that), in a single week.
Taxes at 79%, and sustainable.
Undefefined trade system, and with Trade Goods that aren't traded.
The Drengin, Korx and Korath all having alignment 1, when the Korath should clearly be the most evil of them.
And lots and lots of other stuff.