*Sceptile line was originally supposed to main Giga Drain at higher levels, it seems Leaf Blade was added specifically to help it out. Remember, all grass moves were special back then. Speaking of which, the other semi-signature moves for starters like Muddy Water and Blaze Kick were also not present early on.
*It seems as Blaziken line might have been a more straightforward fire Pokemon, as many physical moves were not included until later. Used to learn Drill Peck, which it can't in the final release.
*Poochyena learned Leer instead of Howl, also learned Screech and Snatch which it can't in the final and learns Thief much earlier. Looks like it was going to be a more technical fighter at first, Migthyena's moveset dummied out at this point in development
*Zigzagoon similarly learned Double Edge instead of Belly Drum, showing that it was originally the aggressive Pokemon(it's original dex entry states as much, with Poochyena being a more cunning hunter). Used to learn Faint Attack, which would have been really useful with special/physical split games. Linoone similarly missing, just like Mightyena
*Lotad only learns Flail, which is an egg move. Much like Magikarp, it might have been a useless Pokemon that was meant to be leveled until evolution. Weird, since it appears Lombre was a completely different and unrelated Pokemon at this point in time and Ludicolo didn't exist.
*Lombre's movesets completely different from final, however it keeps Flail at level 1. I guess it was merged into one evolutionary line at that point after all. Looks really generic, just grass/water attacking moves. Prefer the retail build.
*Seedot only learns Bide. Just like with Lotad, Nuzleaf also learns that move at level 1. Moveset is completely different, looks like it would have focused more on it's dark side rather than it's grass one. Would have been interesting to see a moveset like this in action, looks more physically dependent.
*Ninjask largely the same, however it does know Swift which it wouldn't be able to learn until Emerald. Only different Shedinja has is that it learns Destiny Bond, which it can't in the final(now that would have been busted!)
*Shroomish line largely the same. Dex entry for Breloom mentions Poison Powder by name and it would have indeed learned just that. Not the case in the final, also it looks like Sky Uppercut was added at some point to bolster it's physical movepool.
*Spinda learns Petal Dance over Teeter Dance for some reason and lacks Thrash. Both are horrible decisions, Petal Dance is useless on this Pokemon and Teeter Dance/ a powerful normal STAB attack is one of the few good things it has going for it.
*Wingull was added later on and the movepool here is very rough and early, not least of which in that it learns everything at level 1. Only noticeable difference is that it would have learned Whirlwind. Pelipper knows Bubble Beam instead of Hydro Pump for some reason, making it's water typing even more of a liability in the final game without being able to use it offensively.
*Despite being one of the first new Pokemon to be made, moveset is still very early and it also learns everything at level 1. Wailord did not exist at this point. Same goes for Kecleon.
*Baltoy line lacks Cosmic Power and Rock Tomb, suggesting those moves were a later addition.
*Sableye lacks Fake Out and Confuse Ray, making it much less useful than in the final game.
*Sharpedo very early and learns everything at level 1. Carvanha doesn't exist at this point, confirming my hypothesis that it was a shoe-horned pre evo.
*Trapinch also learns only a few moves all at level 1, Vibrava and Flygon do not exist
*Makuhita line lacks some of it's more distinctive moves, like SmellingSalts/Arm Thrust/Fake Out and has Double Edge instead, a move it cannot learn in the final game. Another Pokemon that was originally much more generic, glad they changed it.
*Spheal was just started, as it has very few moves and they are all learned at a very low level. Lacks most of it's moveset, including Ice Ball and Sheer Cold. Sealo and Walrein do not exist yet.
*Swablu line had a very different moveset, including moves it can't learn like Haze, Mirror Move and Drill Peck.
*Duskull line lacks Will-o-Wisp but has gained Faint Attack. What a disaster, nobody uses this Pokemon as an attacker, and even then there was an evolution just a generation later that did this much better.
*Roselia lacks moves that make it stand out, like Magical Leaf/Aromatheraphy/Grasswhistle. Would have been yet another generic grass/poison type if it released like this, or at least even more so.
*Relicanth learns Flail, which it can normally only learn from Gen 7 onwards. It lacked Yawn and Rock Tomb, making these rather late additions to the game as this is now a pattern.
*Volbeat would have learned Hyper Beam and Illumise would have learned Petal Dance, neither Pokemon can learn these moves in the retail game. Interestingly enough, not only was Helping Hand a late addition despite double battles being planned early on, it seems so was Tail Glow and Signal Beam for Volbeat. Late enough that nobody tested them, remember all bug type moves are PHYSICAL this generation and Tail Glow adds +3 SPECIAL ATTACK. No wonder that a gen 3 entry for this Pokemon remained empty on Smogon until only a few years ago.
*Latis once again learn only a few moves all at level 1. Of note is that they both learn Confuse Ray, something they can't normally do.