Well, I get what you're trying to do, but the fact is that there are just some pokemon that will never be useful under any circumstances because they're just too fundamentally weak and can't be improved (Ducklett), or because the pokemon available are so bad that you just can't win against the next gym leader. I get it though; If you give everyone a bunch of bad pokemon options like when it's time to face a powerful gym leader like Florinia, then then they have to rely solely on luck to win, especially because they can't grind and get overleveled. But for pokemon like Gastly, include them in much later gyms, but not in the beginning. Imagine having to fight Florinia with a team of nothing but the most basic Pokemon?
Personally,because I know some pokemon will be axed, that's why I catch a bunch of different pokemon that will be strong at later levels. Pokemon to include in the beginning gyms would be ones like Slakoth, Sunkern, Pichu, Mime Jr, Oddish, Smoochum, Surskit, wingull, things like that, that can't get too strong. (And of course all the basics that aren't much use later on). Oh and make sure that any Ralts available is a female so no Gallades.
No one's expecting pokemon like Aegislash anytime soon, but I am amazed that you added in Trapinch (Flygon) to this game. People underestimate Flygon, but it can rip holes in teams when i've used it.