There must be some ballance between them Mtrixis. 5 man unit equiped with far supperior gear should hold its own agains a 9 man unit of basic spearman else there's no reason to invest in the weapon gear techs before logistics. I can see that ballance working with 5, 7 and 9 man groups, not for 3 man ones. Which leaves the question why have 3 man groups at all.
No it should not, a 9 man company is at the _end_ of the warfare tree. If you're pitting 5 man groups against 9 man companies, you're losing the military race badly. Could a 5 man group with magic equipment, buff spells, and a bunch of experience levels backed up by a hero last a few rounds? Sure - presumably if you're going 5v9, you've invested in either civics or magic deeply, so you either have a much superior production base AND cool monster friends, or you have more powerful magic, including magic items for those 5 man groups.
Weapon and armor tech gives you access to that gear for your heroes, so yes, there is a reason to do it before logistics (I've done exactly that research path). And lesser numbers can hold their own against larger numbers with better gear, particularly if they're experienced, but not that far apart, you're literally comparing a second level warfare tech to second to last warfare tech (last, really, the final one is a stacking accuracy bonus to your armies).
As for why have 3 man groups: less production, less upkeep, less damage output against weak heroes (and weak monsters). If you started with 5, their damage output, production cost, and upkeep would all have to be tinkered with, and if you're nerfing the 5s, what's the point of removing the 3s?
Early game enemy encounters scale from puny single figures to 3 man groups to 5 and so on, as well as ever-stronger single units - and in theory your heroes ramp up to face those challenges (or your units ramp up to face the heroes, depending on your perspective). The issue right now is that heroes don't just 'ramp up', they launch from a space elevator into low orbit at something like mach 10.
Units have a few other issues too - notably the completely ridiculous upgrade costs to improve their gear.