The Legendary Dogs were first created by Ho-Oh after the Brass Tower burned down to become the Burned Tower. This burning down happened 150 years before GSC. But now the Legendary Dogs have been revealed to exist since pre-history.
We don't actually know this for certain. Sources differ in-game because it's a legend, not established fact, but the three Pokemon who perished in the Brass Tower are simply described as "nameless" by NPCs. Whether they were originally a Suicune, Entei, and Raikou (just as-yet undiscovered and therefore unnamed) or different Pokemon altogether is not clear. There's a relatively popular fanon theory that the trio were a Vaporeon, Flareon, and Jolteon respectively (or even three Eevee) but nothing officially supports this: the idea that they were always Suicune, Entei, and Raikou is every bit as valid as the idea that they weren't.
Pokemon Generations
does show silhouettes of them pre-death in which they're just generic cat/dog shapes, but it's pretty evident that these aren't intended to be existing Pokemon and are more akin to placeholders - if it ever
is revealed in future that they were entirely different Pokemon or forms beforehand, I wouldn't expect whoever designs them to stick closely to this.
Regardless, as the previous poster said, the Paradox forms are intended to be versions of those Pokemon from alternate timelines.
Regigigas created the 3 Regis and has 3 different coloured gems in his body, a colour for each of the Regis that he made. But now we have 2 new Regis that he evidently forgot to make gems for.
It's a valid complaint, but there could be a hundred in-universe reasons as to why it lacks gems for the two additional Regis. Perhaps it's because of the fact it lacks their gems that those two are separate from the others - or it could be the other way round entirely; they separated from the others
because it lacks their gems.
If you
really want to make a connection one could suggest that the yellow pads on its body and the black markings could represent Regieleki and Regidrago but that's pushing it a little. Regardless, I don't think it ruins the mythology in the way you imply. Pre-Gen VIII, the Pokedex states that it made the original three golems - nothing ever said they were the only ones. To put it another way: if I said "I have a son", that tells you nothing about whether I have any other children too.
Slowbro was able to stand up because the Shellder adds weight to his tail. But now he can stand up without that weight even when the Shellder adds weight to his arms.
...where is this stated? The only thing the Pokedex says about on the matter is:
Shield Pokedex entry: Being bitten by a Shellder shocked this Pokémon into standing on two legs. If the Shellder lets go, it seems Slowbro will turn back into a Slowpoke.
Which would imply that Slowking can stand for much the same reason - the toxins from the Shellder gave it incredible intelligence, which apparently covers standing upright. But it's nothing to do with the weight of the Shellder.
See, the Pokedex has its uses, it's not all impossible physical feats and ridiculous claims about heat and light...
Pokémon has been ruined. Gone is the cool lore beind it. All that remains are ruins and randomly shat out Pokémon forms. Pokémon is now GF's litter box. And we are the poop mites.
More than a little overdramatic. I'm unconvinced this post was entirely written in good faith but whatever, at least this reply was interesting to write.