The ideal Robot Master abilities would be focused towards anti-personnel warfare, and a narrow range of defensive abilities suited against the Arsenal we can expect to face, but not against our own weaponry.
Megaman's Mega Buster is an energy weapon, charged with Solar Energy, and he can copy the abilities of fallen Robot Masters. He can be expected to dodge rather than attempt to tank hits. With this in mind, I propose the following ideas for Robot Masters.
Mirrorman - (Ability: Mirror Buster) - A Robot Master wielding Dual Shields, each capable of absorbing and reflecting energy based attacks. Solar Energy is particular is easily worked with, allowing the shields to easily absorb the Mega Buster. Unlike the Mega Buster, it cannot naturally charge Energy to fuel it's own attacks, so it requires an external charge. Recommended to commandeer a facility capable of focusing Solar Energy to create a powerful Laser it can use as a home-turf advantage that it can direct into the Mirror Buster for a Super Move, and otherwise use the facilities as an artillery platform when not directly under threat. Could possibly use advanced targeting software to direct Laser Strikes towards other facilities.
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As an ability, Megaman may use Mirror Buster, allowing him to similarly capture and reflect energy attacks. Our own forces should avoid Energy Based projectiles when possible to minimize the power this ability would have in his hands.
Bunkerman - (Ability: Bunker Buster) - A Robot Master intended as a trap for Megaman. Has only two functions: Bunker Down, and Bunker Buster. It will camp itself in the most heavily defended part of an facility the forces of good would not want destroyed, then as soon as Megaman is sighted heading towards it, it will engage the Bunker Buster. A High Yield Nuclear Charge Device at the robot's core will begin the arming sequence, and it will attempt to sacrifice itself to destroy the entire facility with Megaman still inside, relying on its incredible defenses to avoid destruction and most likely destroy Megaman in one shot. If directly threatened, it may divert charging energy to radiate the room it is in, unavoidably damaging lightly armored targets while it attempts to either outlast or finish charging. It is completely immobile during the arming sequence to allow full power to be directed towards the bomb, however.
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As an ability, Megaman may use the Bunker Buster, allowing him to charge himself up for the suicide bomb. If he ceases the charge early, extra energy will be released in an unavoidable pulse, only strong enough to damage lightly armored targets. Obviously, giving Megaman such a powerful technique will have consequences. Do NOT confront him personally under any circumstances. If he does have this ability, we could deliberately create a doomsday device manned by a robot double to bait Megaman into sacrificing himself to destroy it. If he ever uses the full power of this ability, he won't be around to stop us in the future. We just have to make sure not to personally confront him.
HACKERMAN - THE MOST POWERFUL HACKER OF ALL TIME - (Ability: HACKERMAN) - A Robot Master well versed in the power of AMAZING HACKS. Obviously he will attempt to hack Megaman, and anything else it can turn against him. Hack his dog. Hack the internet. Hack the planet. Hack everything. And if he should somehow fall in battle, he will have hacked his own ability data to transmit a Virus into Megaman's system, where he will have to engage in a battle in the center of the mind to cleanse himself before he destroys everything he cares about.
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As an ability, Megaman will be able gain the powers of the Hackerman. Very, very dangerous if we don't design our hardware around it. As much as Hacks can damage our equipment, as long as we keep most of our systems on closed circuits and 'off the grid' they cannot be hacked. Comms systems meant to coordinate our forces cannot be protected in this fashion, so he may be able to disrupt communications with this ability. Some less-than-digital means of communication may be necessary to bypass this.
Rocketman - (Ability:Napalm Buster) - A Robot Master armed with jet-powered flight and the ability to lay large trails of Napalm. Apocalyse Now reference. He will use high speed jets to avoid direct combat, and simply bomb the crap out of Megaman. If he runs out of Napalm, he will use his speed to leave and go get more. Do not engage directly under any circumstances. There is literally no point in standing and fighting when bombing runs are so much more effective. And will we make him incapable of any form of combat other than dropping bombs just to drive this point home. Basically just a Robot Harrier.
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As an ability, Megaman will be able to rapidly drop powerful Napalm Bombs, and only drop them. They are not suitable as a close-combat weapon, since they actually do require the impact of being dropped from the air to detonate, and if Megaman were to just try to drop them from a basic jump, he'd blast himself. Just in case, however, try to avoid long drops in our base designs, or at least basement designs. Do not fight Megaman anywhere where he could conceivably use the Napalam Buster without hurting himself.
(Note: These could be super dangerous if used in a low gravity environment, like space. Minimize life support on any space facilities, so that the Napalm cannot burn in these scenarios.)
Ghostman - (Ability: Red Phosphorus Grenade) - A Robot Master simply armed with the best sword we can give him, a Sonar System, and a never ending supply of Red Phosphorus Smoke Grenades, particularly well suited to disrupting high quality sensors, so potent that only his specialized Sonar System can pierce it. He will attempt to fill the room with smoke, then attack form whatever angle he can get that doesn't get him shot.
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As an ability, Megaman will be able to deploy these smoke grenades. Non lethal at best, these smoke grenades are nigh useless against the other robot masters. Even Mirror Man, who would require some semblance of finer aim for his abilities, should be able to blind fight a lot better than most thanks to his long-range targeting software that requires a heavy amount of predictive capabilities.
Spikeman - (Ability: Spike Hat) - A Robot Master covered in those goddamn spikes. You know the ones. The ones that instantly kill Megaman. And make him fast as hell so he can most effectively give him a hug. A spike death hug.
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As an ability, Megaman will be able to put those goddamn spikes on his head. The ones that are no threat to us whatsoever, given that we use them fairly often in our levels...just don't try to step on him. Ever.
I'm not too sure what the use for the other two slots.