So some misconceptions:
Specs Exeggutor is the best set, period. It is too slow to take advantage of the ability to switch moves, especially when its strongest move drops its SpA, forcing it to switch regardless. Harvest is a gimmick, I don't care what you say. It is a 50/50 coin flip each turn, unless you specifically set up sun, in which case why are you not using Shiftry and Magmortar. Trick Room is whatever but a well built team will beat TR in general.
There are very few things that can take a Specs Leaf Storm. Most of the things that take Specs Leaf Storm cannot take a Psychic (Weezing, Muk, Scolipede, Vileplume are all KO'd by Psychic easily). Conversely, the things that can take Psychic cannot take a Specs Leaf Storm (Mesprit, other bulky Psychics, etc). All the steels are 2hko'd by Specs Leaf Storm, assuming standard spreads. Special Defensive Altaria (read: 252 hp 252 spd calm/careful) can beat Exeggutor. Defensive Murkrow can beat it with priority Roost and a fairly powerful Brave Bird. That's about "it" that check or counter.
HOWEVER: Exeggutor is weak to all forms of entry hazards. So while yes, every time it switches in, it's getting a hit and/or a ko, it's losing quite a bit of HP with having to sponge the attack and entry hazards. Specs Eggy is hit and run at its finest, but it can only switch in 3-4 times tops. In addition, Eggy has abysmal speed. There are many Pokemon that can outspeed and KO, namely Pinsir, Scolipede, Braviary, Murkrow, Swellow, Cryogonal, Glaceon, Magmortar, Absol, and many many more.
So yes, Exeggutor is an extremely good Pokemon right now. However I still maintain that there is no one force in the metagame too powerful right now. NU is balanced now. There's probably going to be a very large shift next month, but we'll cross that bridge later. For now, can we PLEASE stop bitching about what we think is overpowered and just try new fun sets/concepts? There is a ton to be explored here.