Um, at extreme risk of being a necro (and since it won't make a difference to the outcome anyway) I would just like to point out a couple of things I think were glossed over or misstated. First, I don't think Samus can absorb power-ups or abilities specifically through her grappling beam. I also don't think Tony's suit has a particularly good defense against the grapple voltage. His ZPE field would keep it from reaching his armor, but it would still be draining the power generating the shield. I don't know as much about Iron Man as Metroid, so I don't know if Tony's power source is infinite, but if it isn't that might be a weak point to (eventually) exploit.
However, the bigger point I wanted to bring up is that Samus actually has a hard counter to both his energy absorption and ZPE: she can spam mini-black holes and reality breaking annihilation reactions (unless she's not allowed her MP2 gear in the fight). A ZPE field is incredibly strong, and functions on a quantum level, but both of those weapons break down the laws of physics. Black holes are well known, the laws of space and time collapse at a point of infinite gravity. ZPE can't nullify the effect because gravity isn't energy, it's a mechanism of physical mass. Essentially, since ZPE can't remove the mass of physical object, it can't nullify a black hole, as it's a physical object.
The Annihilator beam might be enough to get past the shield on its own, seeing as how it's an annihilation reaction that uses energy fragments from different dimensions ("light energy and dark energy") as well as/instead of matter and anti-matter in its reaction. Even if the beam itself can't bypass the ZPE field, the Sonic Boom (I always hated the name, I think the listing here calls it the disrupter? much better, imo) would. It creates a tear in space-time, causing extreme damage to anything in the vicinity. That's some pretty serious hax as far as durability bypass goes. It doesn't really matter what Tony is using to protect himself: his molecular structure is just as vulnerable as everything else in the universe when something tears away at the fundamental principals holding it together.
So, maybe Tony has a way of survivng those, I don't know, but as far as I can tell the battle should end with Tony's molecules going through an estrangement of one kind or another.
Again, sorry for the necro. I will go a self-flagellate for my sins and think upon what I've done.