Your problems with the game are just a bit in contradiction with the game's purpose itself.
The game is supposed to be difficult, and you're not supposed to have a set team of 6 to use throughout straight away (considering that the leaders may require certain pokemon to beat). Your problem with having pokemon you don't want in your team is caused by two reasons; one, the fact that not all the pokemon have been implemented in the game yet; and two, that the game doesn't really cater to those who want specific teams, due to how wild pokemon show up in the areas.
The problem is that the game is not meant to be easy in the first place, nor is it meant to be for beginners'; it's purpose isn't twofold, and it's pretty much for those who are experienced with the pokemon series and want a game where the pokemon mechanics work a little differently.
Regarding the Fern issue; that's partly due to your bad luck of moves missing or them hitting you often (poison gas doesn't even have that low accuracy); which nothing can really be done about; and also, you're going a bit overboard with being confined to the grass starter being your worst nightmare, because unless you're horribly unlucky you should've at least caught something like an Ekans or Trubbish, which can kill anything that isn't Roselia in fern's team. The game isn't trying to be gracious; it's not showering you with free potions; it's testing your knowledge of pokemon and your supplies.
And with the first gym; I admittedly was kinda frightened by it too, but for some reason none of my enemies ever exploded; which kinda confused me, but I guess that's just balancing AI? I dunno.
If you've had trouble with this stuff THIS early, then you're not gonna enjoy the later stages. Hoo boy.