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For example, these are the ones I got using Honko's calc (and yes, I did change it to Mega Aggron's base stats):
252 SpA Life Orb Greninja Hydro Pump vs. 252 HP / 252 SpD Mega Aggron: 181-214 (52.61 - 62.2%) -- 98.83% chance to 2HKO

I'm not really sure why you mentioned Focus Blast over Shadow Ball as well considering the latter does more damage even if not by much.
252 SpA Gengar Focus Blast vs. 252 HP / 252 SpD Filter Mega Aggron: 119-141 (34.59 - 40.98%) -- 66.99% chance to 3HKO
252 SpA Gengar Shadow Ball vs. 252 HP / 252 SpD Mega Aggron: 120-142 (34.88 - 41.27%) -- 75.32% chance to 3HKO
(your calcs were a bit off again here; char limit)

+2 252+ Atk Aegislash Sacred Sword vs. 252 HP / 0+ Def Filter Mega Aggron: 130-154 (37.79 - 44.76%) -- guaranteed 3HKO is another that I got that differed from yours

I'm haven't checked all of them yet due to time. I may be doing something incorrectly but it's worth looking into.

1. Your first calculation assumes that Mega Aggron is using a +SpD nature. It's Impish (+Def).
2. You're off base here: I know for a fact that Focus Blast does more than Shadow Ball, and your calcs look way off to me. The calc I posted looks strange because I neglected to mention it was from Mega Gengar.
3. I DID make a mistake here, I erroneously added STAB to Sacred Sword. Thanks for pointing that out.

I didn't mean to come off as hostile when I mentioned this btw. Sorry if it appeared as such. I definitely used an impish nature when I did the calcs, though. I take it you're using Honko's damage calc and you're adjusting the stats to Mega Aggron's new ones, yes?