D'oh, didn't post soon enough to get in the big comprehensive reply....
Anyhoo, Toaster, Your Evil Twin, and I are working on a comprehensive energy weapon de-nerf mod, titled "Future Weapons Today", aimed at addressing the prevailing opinion that energy weapons, particularly lower tier ones, seem anemic in comparison to comparable Guns. We've got some ideas for mods as well. This obviously would be an issue for those using both this and FWT.
It'll also be doing several bugfixes and visual improvements (such as my http://www.newvegasnexus.com/downloads/images/34847-2-1287679906.jpg mod, more http://www.newvegasnexus.com/downloads/images/35678-2-1289695597.jpg, http://www.newvegasnexus.com/downloads/images/35678-1-1289695596.jpg, fixed laser rifle meshes so there's no gaping holes on the bottom, etc). Got some of them done and in-place already.
Sorry - you posted while I was replying; I didn't see it at first.
WMX is basically going to be incompatible with other mods that alter vanilla weapons. Fortunately though, making compatibility patches for it will be
much easier than it was for WMK, since it doesn't have WMK's issue with having up to sixteen times the work for each weapon because of all the extra weapon records required.
While you're here, I was actually going to ask if it would be alright if I used your Awesomefied Plasma Rifle meshes in WMX - like with WMK. The Laser Pistol iron sight looks great too.

Hi there, as MadCat221 said above, we're working on a big energy weapons mod called Future Weapons Today, along with Talkie Toaster. http://www.gamesas.com/index.php?/topic/1139899-wip-future-weapons-today-energy-weapons-megamod/ As well as a big overhaul of weapon stats and so-on, it also features new weapon mods for energy weapons. I'm thinking it would make sense if we pooled our resources. Of course it is possible that we might disagree about what Weapon Mods to add, but I'm sure that there will be areas of overlap. Talkie Toaster's already made a nice Focused Optics upgrade for the laser pistol, so it would be a bit silly if you had to make your own from scratch. And vice versa, would be daft for us to make a laser pistol scope if you've made one. I think Toaster might have made a some Flamer and Incinerator upgrades already too.
When it comes to your suggested upgrades... I love your Plasma Defender ones. With a scope upgrade and accelerated projectiles it will be just like the classic Fallout 1 and 2 Glock 86 that it is based on. And I'm curious to see what your heatsink upgrades for the plasma pistol will look like. We hadn't considered upgrades for the gauss or tesla or recharger weapons at all, those do sound pretty interesting!
I'm not sure about the Limiter Chip Bypass upgrade for the plasma rifle. I never imagined that the reason for a plasma rifle's slow rate of fire was some chip limiting its rate of fire. I figured it was due to needing better cooling or better injectors or better capacitors or something.
The Q-35 Matter modulator has got two sets of "porthole cylinders" on top of the rifle, while the plasma rifle has just one set of them on the right-hand-side. So I was thinking an obvious way to visually upgrade the plasma rifle woudl be to add the second set of cylinders, like on the Q-35. A "Dual Injector System" or "Dual Coolant System" or something.
And in the case of the Multiplas Rifle... that already has a massive capacity of 60 compared to 24 on the ordinary plasma rifle. In Future Weapons Today we were thinking of lowering the capacity from 60 to 48, and lowering the ammo consumption from 6 ammo per shot to 4 ammo per shot or something like that. Anyway, that means that your Dual-Cell Harness mesh woudl actually be perfect for the normal unmodded Multiplas Rifle, since the Multiplas will have double the capacity of an ordinary plasma rifle.
As with (vanilla) WMK, my plan is to not significantly change the stats of the vanilla weapons, since the aim of WMX is primarily just to add more weapon mods. So while I wouldn't want to have most of the features in FWT by default (thanks for the offer though), I certainly don't have a problem with us sharing art assets back and forth. (And like I said above, a WMX-FWT compatibility patch shouldn't be too hard to make.) I haven't got to any energy weapons yet so I don't have anything new to offer right now, but all the relevant meshes in WMK are of course free to use. Grab what you like.

My idea for the Plasma Rifle Limiter Chip Bypass was that the chip was there to prevent the rifle degrading too quickly, since faster firing equals faster degradation. Also, as an internal mod, it was part of an attempt to avoid having an
overwhelming amount of art to do.

Subject to change though, like many of them.
For the Dual-Cell Harnesses, I'm intending to use the 'extended magazine' mesh work I did for the Plasma Rifle in WMK. So that one's effectively already done, if you want to grab it from WMK.
Well if the NVSE guys can make up a function that either finds out if there's a specific mod attached to the weapon or if a specific mod slot (1, 2, or 3) is attached and could add it to the list of enchantment conditions (that is, if you can change it at all), you could make it so that the mod itself doesn't do anything, but the fact that it's attached allow the fire effect to proc from an enchantment on the weapon.
I was also trying to think of ways to make enchantment conditions do most of the work, but I couldn't think up a way to make it so that adding the mod would make it so that that specific axe you modded would have the effect and no others. The ways I thought up would probably add the effect to the base object instead so even axes without the mod would get the effect as well. I think that the fact that mod kits can have scripts attached to them might lead to a way without needing a new NVSE function, but it'd depend on if attaching the mod to a weapon is considered using the object. It could then modify a variable on a script attached to the weapon, but I don't know if that change would only affect the specific weapon or the base weapon. I've only worked with adding scripts to one-of-a-kind types of weapons so I didn't have to worry about whether it affected the base object or not. Still, I don't know if this line of thinking leads to a dead end or if you've already thought of this, but maybe it'll help out in some way.
Ah - now that could be a good idea... though like you said, it requires some more thought. Quite a lot of brain-strain type thought for someone like me, who is not spectacularly good at scripting.

I think the NVSE guys put in a 'GetWeaponMod' (or something) function in a recent beta, too...
Edit:
Ah, it's worth pointing out my stuff is slice & rearrange. It's functional, but by no means comparable to Antistar's work.
A lot of my work is slicing and rearranging too, really.