It all stems back from the very first set, the Base Set, originally printed in English in 1999 - the big red lizard had the most hit points (HP) at 120, making it the toughest Pocket Monster to take down, the highest damaging attack (Fire Spin for a whopping 100 damage) making it the hardest hitting Pokmon without a drawback (were looking at you Chansey with your Double-Edge attack) and had the best resistance, it resisted fighting types by 30 damage, it also has an alluring and unique Pokmon Power which essentially meant any deck could run a Charizard, if you had one
However, there are stronger options available such as Cryptic Command, which offers more flexibility and impact for a similar mana cost
First, if you're already in a theme, for example you've drafted a bunch of support cards, then Baloth Pup is slightly better in your deck and thus you might pick it a little sooner than other players
Each booster box may include alternate art and chase cards highly sought after by collectors
Seeing this card in person makes it easy to understand why it's so valuable, but it's even better when put to use in a strong dragon-themed commander deck