Ok, I'd start by taking out the matter manipulation entirely, or reducing it to only a few very specific functions. In order to be of any utility in a fight, he'd have to be able to transmute several cubed feet of matter in seconds, and that rate would also be affected by the density of the material being shifted as well as the density it was being shifted to, along with the MASSIVE power requirements to achieve the fission necessary to break the atoms apart, then the fusion necessary to put them back together (and somehow prevent everything from exploding). The suit would probably have to be producing more energy than it can safely store in order to power that one feature. As a superpower, atom manipulation is a different issue, but to achieve it on such a scale with tech would be an astronomical feat well beyond the capabilities of a tier 7 suit of armor.
For the energy absorption, I'd start by adding a cooldown for switching between types of energy. For instance, he could absorb heat and electricity, but would be unable to absorb other types of energy for two turns afterwards (during which time he could still absorb the initial energy types, provided they do not exceed his storage level).
Regarding the storage level itself, it depends how long the city could be powered by the suit but it may not be as large an amount as you think. If we could collect all the energy from a single bolt of lightning, we could apparently power all of New York for one second. Technically, that counts as powering a city (and new york is a much more populous city than most). I'd start by giving a more specific example of how much the suit can store, then removing the nuclear explosion ability. That part is akin to Arthur releasing a massive electrical surge upon death that kills everyone within a mile of him. It's overpowered, and really kind of a dick move. If you get defeated, you're defeated. You can't have one last final "F*ck you!" attack that your opponent has no hope of surviving. Instead, just have the suit slowly bleed off the excess energy when it gets close to overload.
Finally, the maximum amount of energy he can hold should not exceed the amount that an equal tiered opponent could exert if they put all their power into an attack (you'll just have to guesstimate this part though).