I must have been looking at it wrong, then, or the wrong thread, or my brain just farted.
And a thousand thank-yous for doing this amazing project!
I don't feel rechargeable ammo is enough to justify the Laser Pistol being outclassed (even against bots) by the Pistol, for which all ammo types are plentiful. Proficiency (Standard 1) is also an excellent investment for all builds; Energy no so much.
I wouldn't want it to lose its annelid weakness, as crippling as that is in the mid-to-late game, when hybrids and monkeys become rare to extinct and the EMP Rifle replaces it against bots.
Do you have the ability to add a little EMP damage to it without reducing its other damage? That way it could at least hold its own in Energy's niche in the early-to-mid game.
Maybe increase its rate of fire so we can increase its DPS without increasing how much damage it can deal on a charge?
Or, and I really like this idea, make it fully automatic so that it appears to be a beam weapon?
I guess this isn't really a suggestion so much as wanting to discuss it a bit, because it's entirely possible you've already done the best possible thing from a limited set of options.
From changes.txt, it looks like you saw two problems: Grenades deal too little damage at the start of the game, and they get more damage than they should from Modify and Sharpshooter later on.
First, how certain are we that that is a bug? Second, what are your options for dealing with this?
I think you would agree that what is currently in the mod is not an ideal solution. It seems to me that putting all of the grenade launcher's damage in the grenades rather than skill level and other factors really overpowers Heavy Weapons 1 and devalues things like Modify, Research and Sharpshooter in a way that was not intended.
If it's a choice between the two, I would prefer going back to the old system and perhaps boosting the viability of the grenade launcher in the early game by adding higher-tier ammo and more of it in the early stages. You seem to have some ability to manipulate the items that are found in the levels.