Writer's block. Time to fish out my pseudo-scientist hat.
I think EXE2's reality - cyberspace overlap event is actually the exact same as the 0-Space. Overdose of server radiation merges two worlds. Overdose of Zero Virus merges two worlds. FM-King Cepheus' immense Z-wave emission turning the real world into waves being very similar.
The thing is, data is an abstract concept. Without a medium, there can be no data, similar to how you can't have a drawing without something to draw on. Now, in the Classic/X/Zero-verse, the existence of a non-physical medium for the storing and retrieving of data becomes a canon fact as of the middle of the X-series, with its existence being likely from the beginning of the Reploid species. This, of course, being the DNA Soul. The events of Xtreme 2 are enough evidence to suggest that DNA souls exist in the material universe as some kind of energy-based storage medium containing the "genetic" data of the Reploid as well as their memories.
In the EXE/RNR-verse, prior to Kotobuki, and after the fact, all data was stored on physical mediums, and cyberspace is a rather abstract representation of the data being stored on those mediums. However, once RNR came into the picture, we had the AM and FM beings, which, like the DNA Soul, represent a non-material medium for the storage of data that exists within the physical universe. However, the wave beings also possess another quality that makes them very relevant to the Kotobuki incident: the ability to convert matter into energy (granted, while ignoring the ratio given by the famous relativity equation) as witnessed by the transformation of humans into wave entities. Now, we know that the creations of humans in the EXE/RNR-verse are compatible with the wave entities, given how RNR Rockman entered physical systems as an Earth-made navi would, so it's not too far of a stretch to make the assumption that the Kotobuki incident ended up re-creating the matter to wave transfer process. Despite the two hundred year gap, we don't see that much technological progress in the EXE to RNR transition. Particularly in the operation of computer devices, they just get smaller.
Keep in mind, as it is a "laser", it should be light based...
If it is, in fact, light it would move at the speed of light. It's likely a similar case to the Star Wars case of turbolasers not being lasers.
Where problems occur is the question of which is the true Gemini Beam: Its representation in the games, or Super Adventure Rockman's take? (Which, I admit, I've only seen from the opening, but it appears to behave like a true laser.)
I'm starting to reckon that what GeminiMan does is literally creating a second version of himself. Not just a fake hologram, but an identical robot with mass, to the point that it becomes irrelevant whichever is real. They're two bodies with one mind and identity. As such both take damage and, when it becomes too hard to sustain two, one just disperses the other and takes over as the main body. An extended variation of this would apply to his ability to create more duplicates in Super Adventure.
This is actually another viable explanation for Gemini Man. However, if Gemini man has another fully operational body, sustaining them both isn't really a problem any more than sustaining one body, destroying one would be a matter of structural damage. Thus, dispersing a body that you spend the energy and materials you created wouldn't exactly make sense. There's also the problem of two brains, which while doubling his processing power, would inevitably create problems.
Let's say Gemini Man creates an identical robot body, doubling every element of his design. For this body to function at the same capacity, all of its autonomic functions would have to be active. Its core would be outputting the same energy, and to control its body, the clone would be thinking, just like the original. Now, this works well because he's a perfect copy of Gemini Man, and thus would behave the same way. However, without some kind of infrared or radio communication between the two, the two may have completely different reactions to the same stimulus and thus step on each others toes, so to speak. Simple enough, add a radio or infra-red modem. This, however, creates a slight reaction time lag, because both copies have to transmit their reactions to the stimulus and come to a solution of what to do. This takes time, which is a precious commodity when you have a homicidal blue robot wanting to kill you and eat your soul to gain your special power. In either case, either coordinating actions or leaving the potential for conflicting reactions, with the addition of more clones, Gemini Man would run face-first into the brick wall of diminishing returns in regards to his combat effectiveness.
Now, there is another option with the perfect clone idea. Only have one Gemini Man "thinking" at a time, and controlling the others via said radio or infra-red modem like puppets. In this case, however, Gemini Man would require a very powerful brain to control another body in addition to his own, and if his currently active body is the one that's destroyed, it creates a potentially lethal lag during which the puppet body's brain has to boot up. There's also an issue with the more powerful processor: To gain that huge boost in performance, Doctor Wily would likely have to overclock the hell out of Gemini Man's processor, which would create huge amounts of heat. This... actually isn't too much of an issue, because it provides an alternate reason for the spikes on his helmet: heat radiators.
... Which creates the amusing mental image of Gemini Man catching a heat seeking missile with his face...
However, even with the hologram conjecture, the question of which Gemini Man is the real one is still irrelevant. It's a principle I like to call Schrodinger's Copy. Another good name would be the Naruto Effect, given how clone battles behave in that series.
Put simply, in a work of fiction, if you are facing four copies of an individual, and you fire three shots at three of those copies, each shot will hit one of the fakes. Similar to the cat in the box that is both alive and dead until the box is opened and the cat is observed, until the shot is fired and connects in a killing blow, each of those images is both real and fake.
The hologram also works with Gemini Man's hatred and weakness to snakes.
Snakes possess keen non-visual senses, and it's likely that Snake Man and his Search Snakes possess IR sensors. Now, a hard light hologram likely possesses a very different infrared image than a solid Robot, and thus a snake would be able to tell which is the real and which is the fake if it is indeed holographic. As for the physical weakness...
... I'll need to think more on that. For now, all I can think of is "LOL game mechanics"
Maybe some kind of psychosomatic reaction?
By comparison, the alien hologram isn't anything solid, just an image overlaying a holographic protector with weapons-mounted. This projector being protected from all attacks but the Bubble Lead by whatever means necessary.
Heh, forgot about the little thing floating around the room after the hologram ends. So it likely does contain the plasma cannon.
The question would be "why Bubble Lead?" (Without resorting to "LOL game mechanics")
We know the projector in the ceiling is a holographic projector, and while it's protected from attack, it also shuts down when the alien is defeated. (On an unrelated note, it's possible the projector played a role in the prototyping and creation of Wily's Robot Masters at the time. The room does look like it would be well suited to that purpose.) While it is possible this is just narrative law in effect, if we look at the weapons Rock possessed at the time we notice something: Bubble Lead is a transparent/translucent looking sphere, relevance being that curved, transparent or translucent surfaces refract light very well.
Jumping into the realm of thinking way too much, each time the bubble hits the alien, the screen flashes. Sure, it's a general damage effect, but in this case it could be thought of as refracted light being scattered about and the projector having to compensate, and to do so, the computer running the system would have to think a bit harder, and generate a little more heat. Eventually, all of this compensation for the effects of the Bubble Lead would overheat the system, causing it to break, thus the loud whine after the battle while the holographic effects are ending.
Doesn't address if it's the orb or the big dome that's projecting the alien, but meh. ^_^
You're all nuts.
You say that like it's a bad thing. ^_^
A twist on beam weapons in Megaman seems to be that they don't sustain shape for long. In Zero's case his saber usually isn't visible when he's not attacking and if you look closely you can see it flicker out after he takes his final swing. My guess is it can only maintain its shape for a short time, thus the user would quickly turn it on only to attack then turn it right back off.
That might actually be a power issue.
Using the Zero example, his saber seems to be separated from his main power source when being wielded, thus returning it to his back, likely to recharge, when not in use.
Yeah, but the fighting poses are still mostly worthless for robots who mix it up close range at least once in a while. Why the heck would humanoid, class SA hunters be imbeciles at hand combat?
*realizes no one cares* 
I need to find that topic...
Uh, but back on topic.
Leverage and force are still science. ^_^
About the plasma weapons thing: I always thought that Zero's saber changing shape when he swings it to be a stylistic depiction, rather than the blade actually curving or changing its length.
True, the X6 sprites for Zero have his saber remaining straight, and the 3D games tend toward the rigid blade.
I suppose stylistic change and technological progress are both equally likely. ^_^