I propose re-naming the tiers, and possibly doing a bit of re-organization. Right now the "mid" tier is not actually the middle tier; there are five tiers above it and four tiers below it (three if you exclude Kanto). I actually think that the Kanto Pokemon could be put into other tiers, so my recommendation would be to make the follow name changes:
upper mid -> upper mid
upper mid -> mid
lower mid -> low
Also possibly rename Electivire and Garchomp to "bottom" and "uber" respectively to reduce the chance of confusion.
Question about Nidoking: when do you get the Moon Stone? It doesn't seem like Nidoking is fully reliant on disposable TMs. Surf, Fire Blast, and Thunder are all decent enough attacks that he could do without Dig.
Pinsir vs. Scyther: Keep in mind Scyther with Technician is pretty solid, though if we go by the 50/50 Ability factor, then I guess Scyther could just go under Pinsir for sure.
I think that Technician Scyther might actually be slightly better than Pinsir. A STAB Technician Wing Attack actually hits Witney's Normal types for only 10% less than a super effective Brick Break, and the boosted Wing Attack is better than Brick Break in a lot of other places. However, Swarm Scyther is incredibly lackluster. Ordinarily, the 50/50 thing wouldn't be a huge deal, but for something as rare as Scyther you don't really have the ability to pick and choose your abilities. Perhaps Scyther should get two separate entries? It's kind of a weird case.
I think that Butterfree (caught during Bug Catching contest) should be a separate entry, ranked a tier below HG Caterpie. SS Caterpie should probably be bottom tier. In SS, low-level Caterpie fails for being strictly worse than a higher-level Butterfree (which can be obtained with ease at that point), and high-level Caterpie fails for not getting Confusion (and the powders) upon evolution.
Slowpoke is really bad. I don't think it's possible to argue otherwise for a Pokemon with base 40 special attack until level 37. I'd consider putting it in the bottom tier. At best, it's one tier above the bottom.
Meowth is basically free items, so any free party spots should go to him as soon as he becomes available. I'm not really sure how you'd tier this. It's definitely somewhere above mid.
Eevee [Espeon]: Not sure where to exactly put him. Under Larvitar even seems weird and keep in mind Confusion is coming off of a skyhigh SpA stat.
I don't think you can get Espeon to learn Confusion, since it would learn it at level 15 (which is earlier than it evolves). I'd put Espeon around the level of Flareon or lower. Flareon gets to start with Fire Blast, while Espeon has no STAB until level 36, which is pretty late into the game. Flareon's Fire Fang comes after Espeon's Psybeam, but it is slightly better and Flareon still has special Fire Attacks until then. (Flareon actually has rather high special attack in addition to its incredibly high attack stat, so it's not like it's struggling before Fire Fang, unlike Espeon who very much dislikes having to rely on physical attacks.) Flareon's Strength is also better than Espeon's Swift.
Gastly (and Abra): When you think about it, Gastly is easier to train than Abra. Consider Abra not having anything until it evolves while Gastly has, while shitty, a movepool. It's easy to train in the Sprout Tower thanks to Hypnosis and x4 resisting Vine Whip. Not to mention that it can switch out if you feel its Atk not worthy enough as it almost allows a free switch.
Abra comes at level 10, Gastly comes at level 3, so it needs less training. It comes after Ilex Forest instead of Sprout Tower. I think that having a Pokemon that doesn't exist for the earlier part of the game is better than a Pokemon that does exist for the earlier part of the game. Gastly actually worse than useless until it learns Night Shade, since it requires time to raise, and it also soaks up "easy experience" that could have gone to something better. Putting something to sleep with Hypnosis and then switching out to kill it seems a lot less efficient than just switching the first turn, especially since Hypnosis can miss.
Gastly's Lick is almost the worst attack in the game. The only move I can think of that is worse than Gastly's Lick is Weedle's Poison Sting, which is 25% weaker and runs off the same attack stat. Having Lick as your only attack until level 15 is just insane, by the time you're around level 10 it will probably be completely unusable. It's also worth mentioning that during the part of the game when Lick can actually kill things, a large portion of your foes are Normal. Sprout Tower is a very small portion of the game.
Night Shade at Level 15, and consider that it probably comes close to 2HKOing most Pokemon that don't resist it (and Normal-types are iffy in common rates at this point).
Abra gets Confusion a level after Gastly gets Night Shade. I think Abra wins there.
Abra joins at level 10 and "gets good" at level 16. Gastly joins at level 3, becomes usable at level 15, and "gets good" at level 33 or until you use the Shadow Ball TM on it. Raising it 12 levels just to "break even" (get something that isn't completely useless) and another 18 levels after that to start seeing a return on your investment seems pretty lousy. If you intend to use the Shadow Ball TM on it, I'd say that Kadabra is actually a better choice for the TM. It doesn't get the STAB, but having a psychic STAB from early on beats having a poison STAB later into the game.