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If you look at the Japanese names, you'll see that it's not just the professors and the SM debuting characters. Please don't question my curiosity.

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Honestly, it's just something that Pokemon does; I don't think anyone but the translators know why.
I'm pretty sure not even the translators know why. They were already named after plants before they were translated.

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Prof. Oak's Japanese name is Dr. Yukinari Okido. Ōkido is a Japanese family name and placename. Literally, big-tree family (Source) .

Thus, Okido is a common family name in Japan. In translation, however, this was changed to Oak, as well, a pun you could say. Oak sounds similar to Okido, and is a big tree. His first name, as said in the above mentioned source, is Samuel, which could be based on the Oak tree at Salem, New Jersey. See the similarity?

After that, it probably became a running gag, a sort of inside joke among developers. Note that it's not easy for people to remember unconnected names. Having them all related so had two purposes, namely, reducing amount of effort required to come up with the names, and two, to make it easier for players to remember. Finally, it gave a sense of familiarity to older players who noticed by themselves that they were all plant names. In a manner of speaking, of course.

That's my take on this. It could be different from the official reason, but this is how it made sense to me. All clarifications/ suggestions are accepted!

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In the Japanese games, every named human character is named after a plant, with the exception of the protagonists, some rivals, and a few other oddballs like Ball Guy. The plants chosen usually relate to the character and their theming. For instance, Misty’s Japanese name is Kasumi. Kasumi means baby’s breath, but it also contains the Japanese words for mist and sea. In English, most characters didn’t have plant-related names for a long time, barring the professors. In Generation 6, however, most of the characters were given plant-based names in Japanese and in English. For example, Clemont comes from lemon, Grant comes from pomegranate, and Valerie comes from the scientific name for rapunzel (it’s a vegetable and a fairy tale). In Gen 7, nearly every character’s name is a plant, and this trend has continued into Gen 8 and likely will continue into future gens.

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