Well, this also depends if you're using the new Super Training feature. But then again, the special stats in Generation 1 and Generation 2 were still more applied to attacks that were more indifferent than the others. For example, a Razor Leaf would be based upon it's Special Attack rather than it's Attack stat solely.
However, when Pokémon Ruby and Sapphire came out, moves were separated by Range, Physical, and Special Attacks. Pokémon Gold and Silver remained with only Physical or more so.. Attack Power. The formula for both game titles are simple a taking it by a grain of salt.
Starters before Gen III and after had around the basic stats for any trainer, old or newbie, to begin and start an adventure. But as the more complicated the games become, the most interesting a starter has an advantage over another person's starter.
Friendship was another stronger ideal in Gold and Silver. If you had your friendship maxed out for your starter or any other Pokémon, this would give you a heavy advantage over someone who doesn't have a good friendship.
As you had stated above:
"Venusaur's special attack is only slightly lower than Charizard's, Charizard is faster but Venusaur is bulkier. the difference is that Venusaur's bulk and moveset allows for stalling"
This being said, it's obvious that Charizard as an average is still better by 1.5% While Blastoise just barely reaches Charizard by a .67% However, stats on the board, Venusaur does have the highest HP Stat. But, Charizard has the Highest Speed, Highest Attack, and Highest Special Attack Stats. Now, Blastoise has the highest Defensive, Special Defensive, and about average across the board. But Venusaur isn't left out that far back, it's the moveset that normally makes the difference with battles.
As you had stated above:
"Same thing applies with Johto starters, although Meganium is the bulky one so it's moveset actually fits for stalling which is great. Feraligatr's physical attack is huge, Thyplosion has around the same special attack as feraligatr's attack and is faster but Feraligatr is bulkier."
Feraligatr has the highest HP and Attack Stat and even with Meganium with Defense, while Typhlosion has the highest Special Attack and Speed, and last but not least Meganium has the highest Special Defense and about even in speed with Feraligatr. Again, it's the same thing as above, Typhloshion averagely beats both. However, again I will state that it is all along the lines of movesets, stats don't make a Pokémon automatically better than another just simply being put
"OH! Typhlosion and Charizard is 1.5% Better than Meganium and Venusuar!"
No.. no... just no. NO! All Pokémon equally have an advantage somewhere, it depends on stats yes, but it also depends on nature, IVs, EVs, and several other things. For example this formula explain hows IVs are calculated into creating a individual stat.
Now in generation two, there was several things added in that changed IVs from the normal 15 to 31. The IVs were changed because of gender, shiny Pokémon, and a few other things including friendship. The formula above remained the same, just a few things were added in. Here are few examples.
Gender Being An Issue:
Shineness Being an Issue: