I've seen a few threads about the weakness/unbalance of various weapons. these include variable setting on las weapons, the subsequent weakening of the bolter, which then getting tweaked made the plasma weaponry weaker again. (These are simply opinions I've seen on other threads)

From this, I would propose:

Keep variable las settings from Only War

For bolters, give felling(x), (please correct me if I've used the wrong word, but my intent is the same) which ignores toughness up to the number x

For plasma weapons, reduce unnatural toughness by one, (and if it has only normal toughness, then it ignores all toughness too)

Las weapons,and other unspecified energy weapons, half toughness, rounding up.

Sp weapons should receive +2 penetration

I envisioned these new changes to try and avoid changing the damage of weapons, which simply cause too much problems. I understand this makes everyone more squishy, but I'm hoping these changes will affect high toughness characters more.

The only problem I have with this is that high agility characters will benefit. However, it does make sense that if you don't get hit, you don't get hurt.

Feel free to point out the myriad of noob mistakes I've made, and how it does not conform to lore and the such. I admit I'm fairly undereducated in the lore, but I'm simply looking from a mechanical point of view.

Regarding your changes:

Bolter: Felling only works against unnatural Toughness in the first place so regular toughness would not be reduced. If you start to reduce regular toughness you would have that scenario you did not want with simply increased damage.

Plasma: That is what Felling would do. Though we have the same problem with ignoring Toughness just being an increased damage that works stupidly good against toughness-shielded enemies.

Las and other: Why even start to affect toughness with them at all? They are pretty decent as of now and the Long Las for example is one of the best early-mid weapons.

SP: A simple Pen increase would be without any reason.

Honestly, I don't get what you wanted to achieve? Your changes would not affect the balance between the guns at all and just make them even more deadly - all of them, something that you did not want.

That SP can be roughly as good as Bolt with its biggest boon being availability is okay, that Las got its great buff depends and the fact that Plasma was always mediocre is the result of the Tabletop.

We have a lot anti-infantry guns as of now but the reason for their existence, the distinctive differentiation between light, medium and heavy infantry of the table-top does not exist in the RPG and this was, besides the less important toughness value, the greatest difference in infantry resilience in the TT.

So lets say we talk about Guard Flak and Carapace. In the RP they have A4 and A6, not much difference. In the table top (5thEd) on the other side they are 5+ and 4+. So a Bolter in the Rp would go right through with his Pen4 just as he would in the TT with its AP 5. On the other side he would still penetrate 4 of the 6 armor of the carapace guaranteed, that is 66% of the armor provided. In the TT though you had to test on a 4+ if the hit actually causes damage and that is still a 50/50 chance.

The RP Version of Wh40k has simply a to small scale in terms of armor and its "guaranteed" damage system makes this even worse. A bolter is super effective in the RP against carapace for it only leaves 2 Armor behind, with your high damage and tearing that is no problem at all. In the TT you have a 50% chance to deal no damage at all. And with higher grade armor this problem even becomes more severe.

Dedicated anti-heavy-infantry weaponry of the TT has no use in the RP system for armor is already absolutely weak and does not require dedicated anti-armor guns in the first place. Sadly FFG realized this and went on the other way with buffing Toughness as a second layer of armor creating huge issues with players that do not like toughness working in that way.

This even more resulted in the issue of weapons like the Long Las being supper efficient (at last in OW with their dedicated talents) shredding even power armor reliably with their additional accuracy damage and the benefits of overloading it with some other talents that increase damage.

So simple question: If you can get your hands on something like a Long Las, that is cheap, reliable and suitable for any situation. For what reason should you even take the problems, acquiring a Plasma Gun that is expensive, quite situational and might even burn your own flesh? - In terms of rules, roughly nothing. Only the RP and personal taste / flavor give these weapons some sort of love.