I think the Aeion abilities if included should be a part of Samus psychic powers.
What about the Scan Pulse? It is more like a long-range mapping function than a psychic power, though it could be activated by those powers at first until she finds how to do it normally or set her suit to do it automatically (something canon!Samus would be envious of, especially if this version also detect potential and known enemy/hostile life or energy signatures along with neutral and allied ones). Okay with the potential upgrade it could get by relying on psychic powers to use precognition to see what is where at that moment, it would be pretty potent... and maybe broken.
Now about the Burst beam, it is simply spamming beam shots, nothing special about it, except it is done faster than one can press the button... but we're not augmented like Samus, so there's that. Or it could be a yet-to-be accessible upgrade for her beams already installed in her Power Suit, so no need for Aeion energy, but again it could be accessed in time of need by Samus via her mind, but then once she uses it she may as well gain the upgrade as a secondary firing mode, unless that was what the Spazer beam was about? If not, how do they (Spazer and Burst) interacts? Spazer becomes the "Hose" (or something else) beam, firing like a stream from a Proton Pack? Okay that would be awesome, especially if it fires exactly like said weapon with the same "projectile". Also imagine just all the reactions and potential jokes that could be done! (Clockblocker drooled for a moment thinking about that, others ran away/threw him into M/S cell or something.)
Lightning Armour would be like what, a reserve energy tank that she learns to tap into at will to preserve her main energy tanks when she willingly or needs to go into harmful areas? Does it even make sense? Phase Drift could be explained as Samus retiring herself slightly from the flow of time instead of stopping/slowing time of the whole universe while she is unaffected like in canon. That ability could be psychic-enhanced/activated with complete understanding of its mechanics, since it may also rely to a point on her precognition. Yeah, we won't see that last one (unless it's used to represent adrenalin boost/bullet time) until much, much later.
Better let the author decide on that one.