Amoonguss can take Acrobatics with its huge bulk then Stun Spore on the thing. Ferroseed can do the same but with Brick Break and a more accurate attack. However, at +2 these guys have trouble. Amoonguss is unable to switch in on a +2 Acrobatics, and if Flying Gem hasn't been used it won't even survive if it comes in at full HP. Ferroseed can also not switch in on Brick Break, but it can survive anything but a crit on the revenge (revenge of sorts).
Bouffalant and Miltank have the bulk to take an unboosted Brick Break and are immune to Grass with Sap Sipper. Bouffalant will straight out kill Sceptile and Miltank will Thunder Wave. These guys do have problems when Sceptile is at +2 Attack.
Entei can use Extremespeed, which can take down a low health Sceptile. This goes for any priority user, but Entei can switch in on Leaf Blade.
Rotom-Fan resists Leaf Blade, Acrobatics, and Brick Break, although it is weak to Rock Slide (Rock SLide isn't often used along with Acrobatics though.)
The best counter though is probably Whimsicott, as it gets priority Stun Spore.