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All of them, even the cutesy Pokemon.
Red and Green had an underlying "treat Pokemon like your partners and not tools if you want to bring out their true strength" message, but the games were mostly set in a semi-dangerous world filled with wild, yet tamable monsters that people trained for sport. The franchise has undeniably been babified since its conceptualization, now being about "love and friendship and the bonds you've made on the way :)))". The tonal shift after the Gen 1 games and the "squeaky-clean family friendly image" being cemented by the end of the Gen 2 era really did a number.
Sure, the games only got better in Gens 3-5, but that doesn't mean that the tone and writing didn't take a huge hit. It only gets worse with age, too.
