Hunter J was definitely a trainer, she sent her salamence and drapion out of pokeballs and had them use moves against other pokemon, that's like a textbook definition of a pokemon trainer.
Also coordinators are really very similar to league trainers, they have several set places to travel to and challenge, they eventually battle under controlled conditions, they end in one huge conference which is on TV to earn a title of champion/top coordinator. Compared to the other roles (breeders, coordinators are among the most like gym challengers, any many coordinators like Dr Abby, Erica, Kelly, Marina, Zoey, Ursula and Savannah all could be powerful in battle. Besides, there are also lots of female trainers in every pokemon league with mixed degrees of success,
Even in leagues female characters are prominent, Ritchie and Gary loat to women in the Indigo conference while Ash struggled against Jeanette, Macy got a couple of episodes in Johto and beat Jackson, Katie was excellent in Hoenn and Bianca got focus in Unova. Then there are wise characters like the Latias Nurse Joy (in fact lots of Joys are really strong) and Juniper, as well as movie characters like Neesha, Kidd Summers and Juanita.
I'm not worried about them making a weak female protagonist, I'm worried she'll have a boring or poorly defined goal or that too many of her episodes will revolve around ship-tease that will never really go anywhere. That's why I wish Alexa had been a protagonist in Kalos, she'd have been unique as an older female travelling with Ash, would likely not have had ship-tease with Ash (who hasn't shown definite romantic interest in a girl since episode 9), she's knowledgeable enough to fill the exposition role and she can travel with Ash while looking for big stories so it would feel natural for them to travel together. Hopefully someone like her can be a companion this time.