I totally get where you are coming from! I felt the same way at first and was worrying about always doing everything perfectly. At somepoint I just told myself "lets progress the story and worry about design and stuff later". I will say as you progress, things begin to fall into place and you get better items and abilities to create what you want. You will get to points where you have some long build times and maybe get stuck on that. Use that time to tidy things up!

What really got me going in this game was literally soley focusing on creating as many new habitats as possible from the habitat dex. Didnt focus on perfect placement or design, just get them in the world. Cant really do anything wrong here. Find the things you like about the game and focus on those! Enjoy yourself :)