Zero's powers
Megaman Zero in recovering his memory also recovered the use of all of his previous attacks and skills. I tried to show this partially in the Battle scene during the Doctor and Zero.
Powers used in that scene
Dark hold froze the collapse and stopped the fall of Ragnarok long enough for Zero to kill his enemy. Its show many times in game that the new world has much more rampant energy. This is shown in the attacks, since normally special attacks consume energy from a POWER BAR which is totally absent in this game. My personal logic being that Zero era (and equestria) have large amounts of magical and Electrical energy that's free flowing and wild.
Megaman X6 saber boost chips. (logic being that when he sealed himself Zero gave his, at the time current Saber to X who then returns it. I assume the chips became permanent in the weapon and he merely needed to remember how to access them. These are how he was able to cut down and deflect energy attacks. In equestrian, he will be able to Cut magical energy and magical attacks the same way.
Omega Aura: initially shown during the BAD ending of Megaman X5 with Eurasia succeeding in hitting the world. To put it simply Zero surrounds himself in his Virus energy and it was enough to rip through the Flimsy barriers (which where the weakest of Wile's attacks, a single buster shoot took them out)
Story line train of thought
I'm up for suggestions here honestly, The only set stuff in mind is that the entire group is in love with itself. But that's a parody on the MASSIVE shipping stories here. Taking notes from some other stories, Zero will discover Non pony places he can explore that will function as ROOMS where he will interact with X and Co.. I'm already planning to have X and Celestia already knowing each other. (it fits X's Know everything and after I found out about Trollestia it sorta reminded me of Cyberelf X anyway.)
AS Zero grows in the Pony world he will adapt and grow in talents, leading to Special challenges involving the 4 guardians to master their forms. HE can already use them but he needs the challenges to truly master them. [In reference to How form are obtained as well as Weapon Skill learning in all Zero games. By beating challenges, and constant use.]
Feel free to comment on this chapter if you have Questions or such about the story and if they are not too spoilerish[totally not a word] ill answer them ^_^ hell even if they are spoilerish[still gets use though X_X], its not the destination its the journey right?