The problem with RPG Maker is that it is just very limited in some ways so you can't fully avoid that your game will look and feel like an RPGMaker game to some extent, no matter how much effort you put into it.
But I think that's okay - yeah, there's definitely some stigma around RPG Maker, but I've seen some very fun games made in it, and there's some very critically acclaimed RPGMaker games too.