Secret Pokemon would be hidden just in case. it would be Suicune

Meloetta is legendary

I just hope you aren’t going to inbreed your Pokémon. It’s illegal in the real world, you know. :p

But again, that’s the anime, this is real life.

Tobias also had a Latios and if the Greatest Everyday battle was canon, he has a Entei and a Lucario as well.

Legendaries don’t kill in the anime (Azelf doesn’t count), but in real life, what do you think would happen if your Groudon used Fissure in a random battle near your local mall?

Also, Rotom isn’t a legendary ._.

I’d probably want:
Alakazam
Dunsparce
Blaziken
Vespiquen
Minccino
Ditto

Ditto would be nice to sort of “expand” what I could have, and for breeding purposes, I suppose.

Try to think about it realistically.
Do you really advocate the concept of a ten-year-old owning the creator of the sea (Kyogre) and/or the master of time (Dialga). You can catch them in the game because the purpose is “to catch ’em all,” and regarding the anime, it’s meant for a younger demographic who care more about flashy giant monsters as opposed to character development and a solid plot.
Honesty, there are even “regular” Pokemon that would be uncommon in real life, such as Volcarona and the starters.

If it was with the gens we grew up with I would have Charizard, Lapras, Magneton, Aerodactyl, Snorlax and Dragonite

To be honset, this fluctuates from time to time. However, with direct attempts to keep the cliche down…

Swampert
Manectric/ Houndoom
Swellow
Aggron/ Torkoal
Skuntank/Cacturne/Exploud
Torterra
And… Mostly Gen 3. Eh, I grew up with that one. It fits.