Bots can still ignore captcha and anti-cheat software like gameguard. So one of the best solutions for a game of this quality is to just put them behind a pay wall or an RNG lootbox system. Once Scion classes come out, you'll be less likely to see people complaining about "pay to win" or not being able to trade, as Scion/Successor classes are extremely overpowered in comparison to normal classes. But because they cannot have sub-classes, I can expect them to be a little stronger than them.
SWTOR used to be a pay to play game, mind you. Freemium is still not "True Free to Play," either. Freemium means that certain features of a game are locked behind a pay wall, one-time purchase or subscription. I don't want PSO2 to turn into Vindictus or Continent of the Ninth Seal (C9) either (both of which are instanced / lobby-based MMORPGs like PSO2), so I think the premium service is fine as-is.