Whilst it is true that ninja do not appear in modern warfare, to say that nothing like them now occurs is false. Ninja held true to what is nowadays conventional warfare - stealth, camouflage, and advanced tactics, the modern day "ninja" equivalent is that of a covert operative in a group such as the SAS, serving greater tactical roles without messing around like a moron with shurikens (which were actually appallingly inaccurate) when a well placed pistol complete with silencer got the job done far more easily.
However, this "niche" of the ninja rather empty in X-Com, and could easily be filled by a stealth camouflage light armour (similar to Schwicks armour caste) and the related tactics it allows - from invisible snipers to small arms/melee "assassin" units for sneaking up and stunning/slaying targets protected from more usual arms fire (or at least cheaper than using a fifteen blaster bomb spread to blast through all cover) - seems more than apt for the X-Com setting, allowing a trade-off on protection for extra suit design, rather than the typical "3 beats 2 beats 1 beats 0" armour system the first two games worked on.
Secondly, I notice much scorn on the notion of "dedicated" melee weapons; When it comes to overall armour penetration, quite right, human muscles aren't the most powerful effectors out there, even the katana - widely accepted to be the most advanced development in melee combat ever invented - cannot reasonably hope to penetrate even basic alien alloys.
However, with the dawning of energy weaponry, so too comes a revolution in hand to hand weapon design, for with almost every form of advanced energy, it is easier to generate the energy at short range in a contained form than to project it at distant targets (hence why a blowtorch is hotter than a flame thrower). As a result, short range energy weaponry will be able to project far a more focused and devastating power-stream than an equivalent-sized projectile weapon.
Let's take the laser for example.
To successfully utilise laser weaponry in the form of the pistol, a power source is needed, refinement and containment to maintain the integrity of the laser over often very long distances, the longer the barrel can be, and larger the "clip" - or power source - the greater the potential focus of, and supply of power, resulting in bigger weapons being more damaging and more accurate.
However, with a short range, self contained system of a laser projecting to a nearby receptor point, the level of refinement can be much, much lower yet still have the same strength beam.
As a result of this, in a close range equivalent of a melee laser weapon to the same "two square" scale as a pistol (basically, a laser version of the popular "army knife" idea), the power supply can occupy not only the "clip", or handle, but also the majority of any blade, which would be shaped in such a way as to accomodate a single "edge" where, upon activation, a single laser stream would be projected from hilt to blade tip.
So, due to the change in power output, a 2 square lasknife, though it lacks range, actually has the equivalent power roughly similar to the laser rifle instead - Just short of seventy.
Extend this concept to a blade the size of the laser rifle, where a stronger beam actually needs MORE, not less, attention on focusing that energy through the barrel, once again a problem far less limitting to the close range laser sword, which can again project a far more focused beam once more.
If we are generous and assume only one third of the laser rifle's construction is on the onerous task of getting its payload from muzzle to target, then the laser sword, with the majority of force dedicated to simply generating and maintaining short bursts of highly concentrated beams, the weapon nears 90 in attack power.
This is a multiple of almost 1.5 per size range. A complete jump A laser "axe" or similarly sized weapon of Heavy laser size, following this formula would feasibly be gifted with a power of 125, though at this size, it starts into the "heavy thermic lance" territory, and slowing down agents trying to get close enough to start swinging. However, this also stands second only to the Launcher, and hasn't even visitted the possibility of plasma weaponry (and probably won't, given the timeline delay before plasma swords come into play).
This brings forth a brand new tactic as well, with the general TU% cost for a single hit ranging from 5%, to 7%, to 9% to keep it roughly in line with TFTD equivalents, do you shoot that Morlock lurking in the alleyway with an autofire Heavy Plasma, or do you fly over the building, drop down behind him and slit his throat with superior sword penetration and still have TUs left over for reaction fire with your "ninja" laser swordsman? What about that arthopod? And while you're at it, why not just a laser bayonet laser rifle? Or skip it entirely whilst you build even bigger guns?
I think there's plenty of room for both stealth kills and really cool sword things in X-Corps, and in the end, isn't that what being a ninja is all about?
(Ah yes, and if it comes to a ninja mod, you think it would be possibly to change the beserk to "n% is flipping out!"?
As usual, feel free to comment on my ever so slightly off kilter ideas.