CHECK <not a hard counter as originally said; see below :( >
Manectric-Mega @ Manectite
Ability: Lightningrod -> Intimidate
EVs: 48 Def / 252 SpA / 208 Spe
Timid/Modest Nature
- Overheat
- Volt Switch
- Thunderbolt / Protect
- Hidden Power [Ice]
The given speed EVs outspeed MegaMetagross of course, but also allow MegaMan to outspeed Greninja, Revenge Killer Alakazam, Garchomp, Dragonite, and Gyarados (even at +1 for the latter two). In general it can outspeed most non-scarfed threats in the meta. The spare EVs are invested in physical bulk to help Manectric better tank hits from Metagross and avoid death by hax.
Manectric can switch in on the indicated set and threaten a 31.3% chance of OHKO with Overheat. MegaMan really needs to be preemptively evolved to do his job, however, and if he switches in on Zen Headbutt he may need to consider Turning out to build up -1s on attack to get the kill since Zen Headbutt is a 2HKO. Switching in on any other move, however, allows MegaMan to 2HKO with an Overheat/Volt Switch combo.
I've thus slashed Protect, because if MegaMan isn't already Mega-Evolved, he is outsped by MegaMeta and risks getting killed. If you are going to lead with it or have a way to get it a free switch, however, it can do its job even with the outsped turn nailing it for tons of damage. Because of all these maybe's (the risk of hazards or chip damage or switching in on a ZHb, the problem of Overheat not being a clean OHKO, the necessity of being evolved), MegaMan is only a check.
The Timid nature is recommended to ensure MegaMan can continue to do its normal job on your team of being a VoltTurn harasser, Greninja check, and general speedy nuke, but a Modest nature gets that Overheat up to a 87.5% chance for the OHKO and might be worth it if you want MegaMan purely to make Metagross's life miserable.
Calcs:
252 SpA Mega Manectric Overheat vs. 0 HP / 4 SpD Mega Metagross: 268-316 (89 - 104.9%) -- 31.3% chance to OHKO
-1 252 Atk Tough Claws Mega Metagross Zen Headbutt vs. 0 HP / 48 Def Mega Manectric: 142-168 (50.5 - 59.7%) -- guaranteed 2HKO
-1 252 Atk Tough Claws Mega Metagross Meteor Mash vs. 0 HP / 48 Def Mega Manectric: 80-95 (28.4 - 33.8%) -- 0.5% chance to 3HKO
-1 252 Atk Tough Claws Mega Metagross Hammer Arm vs. 0 HP / 48 Def Mega Manectric: 119-141 (42.3 - 50.1%) -- 0.4% chance to 2HKO
-1 252 Atk Tough Claws Mega Metagross Ice Punch vs. 0 HP / 48 Def Mega Manectric: 90-106 (32 - 37.7%) -- 93% chance to 3HKO
and just for good measure:
-1 252 Atk Mega Metagross Earthquake vs. 0 HP / 48 Def Mega Manectric: 180-212 (64 - 75.4%) -- guaranteed 2HKO after Stealth Rock - MegaMan can live and fish for that OHKO even under a worst case scenario that isn't in the listed st.