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Basically, the problem is that Sceptile is clearly a lizard with some anthropomorphic traits, while Inteleon looks more like a human with some reptilian traits. Sceptile's body shape, leg design, claws, and proportions are all satisfyingly reptilian, while Inteleon has none of those. Its stance is humanoid, its limbs are humanoid, and its proportions...are a diaster.
It's annoying because Inteleon is so close to being a good design, but just isn't there. A lot of people hate how thin it is, but honestly, the idea of a whip-thin lizard Pokemon is pretty cool, it's just how its used that's the problem. Imagine an Inteleon that stayed rail-thin, but had hands, feet, and a head that suited it proportionally, and appropriately digitigrade legs. Imagine an Inteleon with reptilian claws instead of creeper hands. Make it so that it spends a lot of time on all fours. It could keep the spy theme, but it would ditch the James Bond motif to focus on stealth. Make it a physical attacker, and ditch Snipe Shot and replace it with a move where Inteleon goes invisible, sneaks behind its opponent, and attacks with its tail. It could keep its boosted crit ratio, but instead of bypassing targeting abilities, it could hit through Protect like a one-turn, Water-type Phantom Force.
Inteleon is frustrating because it has the makings of a good design, and would only need a few tweaks to get there. But it just isn't there.