List of Pokemon that pretty much always come out on top against it:
LO Excadrill
And a lot more.. not to mention since Venusaur is a wall it doesn't do much damage in return.
That being said Mega Venusaur is a great Pokemon because it can still take on a lot of attackers and Leech Seed if your opponent lacks a grass type or it's dead but S-rank is too high of a rank for it. A rank is like the perfect fit for it and I'm not changing my mind.
252+ Atk Life Orb Mold Breaker Excadrill Earthquake vs. 252 HP / 252+ Def Mega Venusaur: 149-177 (40.9 - 48.6%) -- guaranteed 3HKO
0 SpA Mega Venusaur Giga Drain vs. 4 HP / 0 SpD Excadrill: 136-162 (37.5 - 44.7%) -- guaranteed 3HKO
Excadrill doesn't even beat the most common variant of Mega-Venusaur. What are you talking about?
Also I think you expect far too much from Mega-Venusaur. 80 / 123 / 120 with reliable recovery and good defensive typing is
amazing, and 122 Special Attack is actually crazy for a wall to have. How many of those "Mega-Venusaur responses" would not mind switching into Mega-Venusaur's unresisted STABs, let alone do so more than once? 80 Speed is not even slow for a wall: -Spe natured Mega-Venu still outspeeds 0 Spe Skarmory.
Leech Seed is only part of the equation. Despite having access to a wide variety of useful moves, Mega-Venu doesn't actually have 4MSS. So long as you have Synthesis, any combination of Sludge Bomb, Giga Drain, Sleep Powder, Earthquake, Leech Seed, or even Roar, and Mega-Venu will still be doing its job wonderfully. I think the problem is that the Mega-Venusaurs you faced / used keep spamming Leech Seed on the switch instead of say, hitting the switch with a 90 base power STAB move off 122 Special Attack that can induce poison, which would likely prevent or deter them from doing it again.
Mega-Venusaur is damn simple to use, brings great rewards with little risk, takes on a myriad of threats singlehandedly (how many Grass-types do you know can beat Ferrothorn
and Goodra one-on-one?), and is easily customizable to the team's needs. S-Rank up the wazoo, baby.
Edit: and now for your "responses", provided Sleep Powder has already been used.
Latios: need Psychic moves to actually do anything lest Venusaur stall it out. Even Trick doesn't work, and Sludge Bomb hurts.
Latias: If Venusaur has Roar, Latias isn't getting anywhere. Sludge Bomb and Leech Seed will prove annoying as well.
Choice Band Talonflame: Sludge Bomb wrecks it on the switch, but does force it out.
Choice Band Victini: Earthquake gets it as well as Sludge Bomb. Forces it out too.
Mega Pinsir: Sludge Bomb, force out.
Kyurem-B with or without Sub: Sludge Bomb is taken relatively well, but poison will be annoying.
LO Excadrill: outright loses to physically defensive Venusaur.
Reuniclus: Sludge Bomb still hurts, but at least it's immune to residual damage. Being slower can be bad though.
Alakazam: same as Reuniclus, but trades bulk for speed.
Deoxys-S: Sludge Bomb, force out.
Heatran with or without Taunt: Earthquake
.
DD Mega Tyranitar with or without Taunt: What? Those
powerful Giga Drains & Earthquakes will take you down before you can get strong enough o do the same.
DD Mega Charizard X: Sludge Bomb (EQ if already Mega'd), force out.
Gliscor with Taunt: Giga Drain beats Gliscor one-on-one. Hell, Mega-Venusaur is a Gliscor counter.
Togekiss: Sludge Bomb ouch.
Espeon: Anything ouch.
Xatu: Sludge Bomb ouch.
Mega Charizard Y: Sludge Bomb, force out.
Mew: like Kyurem-B, favorable but poison hurts.
Sub Disable/ Taunt Gengar: I'll give you this one, but Leech Seed is still annoying.
Sub Roost Pressure Kyurem: Poison and Leech Seed hurt its staying power. Also there's Roar.
Volcarona with or without Sub: Same as SubRoost Kyurem.
Celebi: Sludge Bomb ouch.
Yeah, almost none of them can do this over and over.