I personally like that some enemies require some effort to kill, especially personal/power armor and the more advanced enemies (provosts, church exalts). It creates a situation where you have to sneak around and either wear them down with crappy weapons and acid flasks or hold/avoid them until you can bring the right thing to bear. Weapons kill, but primitive weapons shouldn't kill advanced enemies, at least not as well as advanced weapons.
As it is, weapons that scale outclass those that don't. We get so many missions that gals improve much faster than tech improves. This is assuming you manage to keep the gals alive, of course. But it is doable, especially once you get decent armors, more hp on them veterans and dog scouts. It is especially easy now that early game enemies have been nerfed and that you can raid awesome defender armors in the early game. (Note on raiding armor: I would make it so that only traders and academy can carry defender, and even heavy armor, with some decent crew to protect it that wear armor similar to what they transport. Spartans should carry camo gear, tac vests and tac armors. Raiding spartans for defender armor begs the question: If they can carry it, why don't they ever wear it? or at least the lower tier tac armor).
The way to improve guns damage is to research better guns, but that takes a LONG time. Let's take second tier ballistic weapons: You need the proper drops from enemies to acquire the guns in the first place (light/heavy/auto-cannon, LACC, CAWS, which don't drop that early in the game probably due to itemlevels) and then producing the ammo is non-trivial too. Eventually you get to tier 3 ballistic (with the custom/smart weapons) but these still aren't doing as much damage as the primitive bows and knives (haven't tried javelins yet). Since I don't want to play "prehistoric cavemen raiders in the future", but "Piratez of the future", I tend to go for gunz, and lately the super slow pace of gun improvement compared to the stat-wise tempting, fluff-wise uninteresting (to me) primitive weapons, has been wearing my interest down. (Yes, it is my own decision that makes it so and that's why I didn't mention it before, but you asked for opinions).
By opposition, the way to improve with bows and knives is easy: you just have to use them and you can bypass a whole lot of the tech. Eddie's claim that his Fuso Knives are better than a gauss pistol (at short range, of course, but they are both somewhat short range weapons) shows it is a bit crazy. Sure a ninja gal can do tremendous damage with a Fuso knife to the enemy's face/weak spot, but why can't a gal do that with a pistol shot to the same place? Throwing weapons also improve your ability to use nice long range explosive throws.
I've said it before and I'll say it again: I agree that it makes sense for primitive weapons to scale with both accuracy and strength since you pull the bow further/throw the knife harder if you are stronger, while guns scale only with accuracy since your gun doesn't fire more powerfully because you're stronger (but hopefully you can carry a bigger gun, and actually you can handle the recoil better so.. better accuracy on some guns from strength? hum..!). But the current situation does not work very well with:
- Bows/Knives: Hit more with accuracy, hit more often per turn with TUs because of flat rates, more damage with both accuracy and strength while keeping the same weapon
- Guns: Hit more with accuracy, more damage only from changing weapon
Primitive weapons scale 4 times as much as guns for a given weapon! (actually, it is multiplicative, not additive, so it's even more). If gun damage also scaled with accuracy or reactions (and I know you are doing this for some), it would help.
Case in point: Bows get a whopping 50% bonus from accuracy and with a few research projects, you get an extra 40% str. Sure they start from zero, but it is easy to catch up. A longbow with 60 throwing accuracy and 55 str will do 60*0.5+55*0.4 = 52 damage, which is the same as a laser rifle with the best clip, it will also hit at pretty much the same accuracy (120% instead of 125% for the rifle), fire at a flat 40TUs (so eventually 2, maybe 3 shots) compared to 60% of TUs for the rifle (only one shot/turn ever), and it will never require ammo compared to requiring fancy ammo and lots of research. It also works really well combined with Fuso knives for short range which outdoes any pistol in damage by the time you get 80 throwing accuracy (at which point 0.75*0.025*80^2 = 120% to hit on snap shots if I read that right). Arcing shot is usually a good thing too, except for breaches (which are short range -> Fuso knives domain) and base defences (again, Fuso and melee work well here with hit and run).
All that to justify these suggestions:
1 - Buff guns a bit with some accuracy/reactions to damage, to help them keep up and represent the ability to aim at weak spots.
2 - Might be cool to play with gun damage and damage roll to make them more reliable than primitive weapons (ex.: +33% damage & damage roll 50-150% damage -> damage is now 66-200% of original damage instead of 0-200%).
I also agree with Eddie's suggestion of:
3 - Changing the primitive weapons formula so that they plateau after a certain point, to prevent them from outclassing high tech weapons (at 100 throwing + 80 str, a longbow does the same damage as a gauss rifle, can be aim fired for a similar TU cost as the rifle's snap shot but with way more accuracy. It's just missing the reaction fire)
4 - Making armor more effective against primitive weapons. An arrow or knife shouldn't have the penetration power of a bullet. Maybe it's going to hurt a naked target more (it's bigger afterall, and may have more momentum/energy from its larger mass despite its slower speed, but size is also a disadvantage when it comes to piercing armor where you need to concentrate the impact as much as possible)