There are so many things that can kill Exeggutor of I will only mention the most common Pokemon/strategies.
First of, Fire types. Pokemon like Charizard and Heatran will easily finish it of with almost any Fire move, especially if the Sun is up. MScizor cant do anything about Fire types, and Greninja is also going to struggle if the Sun is up
Secondly, Bug types, or most notably Scizor, Pinsir and U-Turn users. These can easily pick Exeggutor of, whilst Greninja/MScizor cant do to much about it. Exeggutor is just to weak to Bug attacks to be able to take them on, even with team help.
Almost any sweeper or tank that cant be killed by Greninja/MScizor in the first turn will be able to finish Exeggutor of. This include Dragonite, Heracross, Mamoswine, Aegislash, Togekiss, Cloyster, Bisharp and many more. Sure, some Pokemon with an unfavourable typing such as Psychic or Grass might not be able to kill it, but anything that isn't directly threatened by Exeggutor/Greninja/MScizor will be a major danger.
Any sweeper that's faster than Greninja/MScizor. Basically the same as the last point, anything that outspeeds Greninja/MScizor, either naturally or by using a Choice Scarf, will be able to threaten Exeggutor. This include but isnt limited to Noivern, Scarf Gengar, Scarf Landorus, Scarf Scizor, Noivern, Accelgor, Aerodactyl, Crobat and Swellow. There's many more, to many to list if were including Choice Scarf users.
Lastly, Talonflame deserves a special mention. Its Ability, along with Brave Bird allows it to pick of Exeggutor like a sitting Ducklett.
Overall its not difficult to counter or check Exeggutor, and there's simply to many different things that threaten it for a single teamamte to be able to counter them all, especially in doubles. Im not saying that you shouldn't use it if you really like it, but there are far better Harvest and Sun abusers out there, such as Trevenant and Venusaur, and Exeggutor just need to much maintenance to be able to compete in serious competitive battling.