It may be versatile and whatnot, but it's very frail and can be dispatched of by quite a few pkmn.
Some examples:
Gurdurr @ Eviolite
Ability: Guts
EVs: 252 HP / 252 Atk / 4 SDef
Adamant Nature
- Mach Punch
- Drain Punch
- Knock Off
- Ice Punch
Most of the time is able to afford an Eviolite being knocked off because Gurdurr has decent bulk anyway.
Granbull @ Leftovers
Ability: Intimidate
EVs: 252 Atk / 252 HP / 4 SDef
Adamant Nature
- Play Rough
- Earthquake
- Heal Bell
- Thunder Wave
Intimidate makes Shiftry useless against Granbull unless Leaf Storm.
Slurpuff @ Sitrus Berry
Ability: Unburden
EVs: 200 Speed / 252 SAtk / 52 HP
Modest Nature
- Calm Mind
- Draining Kiss
- Flamethrower
- Psychic
Knock Off that berry, activate Unburden. gg.
The thing is however those are all checks to the physical version. Once people start realizing the nasty plot demolishes its physical set's checks, people will begin running nasty plot. Here are calcs after shiftry gets a nasty plot up:
+2 252 SpA Life Orb Shiftry Extrasensory vs. 252 HP / 4 SpD Eviolite Gurdurr: 406-478 (108.5 - 127.8%) -- guaranteed OHKO
+2 252 SpA Life Orb Shiftry Giga Drain vs. 252 HP / 4 SpD Granbull: 372-438 (96.8 - 114%) -- 81.3% chance to OHKO
+2 252 SpA Life Orb Shiftry Giga Drain vs. 52 HP / 0 SpD Slurpuff: 316-372 (99.3 - 116.9%) -- 93.8% chance to OHKO