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I'd be fine with almost all of them, really. Just not a fan of the proto dogs or the amount of kinda useless pre-evolutions (since a majority of the mons that had cut prevos were already early game mons statwise so I don't see the point of putting a prevo of it even earlier on. Granted they could've tweaked the stats, of course.) The ones that I really want though (along with anything I'd change about them for present day) would probably be..
The wolves, super cute. Nothing much changed here. Slightly tankier alternative to Sneasel/Weavile that you'd get around the same time, probably has Fur Coat to up it's defense even more.
Tiger-Balls. Keep the first stage mostly as is and maybe redesign the second so it isn't just a case of "it just gets bigger". Maybe make the line a two way path? You can either evolve your mini-tiger ball into a fat tiger ball and give it beefy defenses or evolve it into a typical super fast but frail as hell sweeper. Or just make it a three stage line in general and say the second stage stuffs its face with electricity so much it's gotten super fat, but by the time it hits it's final evolution its body adapts and is now super fat. Also lets the second stage use Eviolite.
Spurdo. Separate it from Porygon and just make it some silly plush mascot. No doubt a shitmon due to it's stats, but I wouldn't be surprised to see it get shit like Prankster for the support cheese.
Qwilfish, Farfetch'd, and Pinsir Evos. Self explanatory, both need it (though it's a bit too late due to Mega-Pinsir.) Qwilfish and Farfetch'd for the stats, Pinsir to match up with Scyther again. Shocked to see Qwilfish's evolution got cut, honestly.
Vodoo Doll+Pangshi: Neat concept and I love Pandas. 10/10 would use even though it'd probably end up being a shitmon.
Octillery: Bit on the nose but it's funny as shit. Remoraid's design got changed and Octillery's probably followed suit soon after, but at least it could come back as a Mega.
Inb4 autism.