Hey there. I want to let you know that Iove the enthusiasum you have for this game!
If the problem with your spriting is that you're using the program paint, may I suggest using a free program called Krita? Its very similar to photoshop and its completely free.
Congrats on doing this work by yourself! Its really hard to complete a full game by yourself.
Please consider googling pokemon tilesets deviantart free use/public use to see if anyone has posted anything up for grabs to use publicly, I know I have found a few on there so far. It will really improve your game.
The indoor tiles themselves look fine to me most people use those types. Just try to decorate them more and people should be happy. There are a few indoor tiles on deviantart you can grab also, it helps make things feel "new".
what I would do with the sprites you've colors is, put them in krita, choose a similar color pallette, and add some definition to the clothes themselves, for example, make the girls dress have a line that shows "wavyness" if you know what I mean.
Using paint is actually making your life harder. I know its a pain to learn a program like Krita, but it can help you a lot in comparison.
What would I do with the larger character sprites that show up before you battle? (i.e. the giant faces) is that I would go on the internet, grab an rpg face in the position you want, and change the hair and eyes etc and add the clothes you want. Then you'd have a more professional rpg anime face to go with your outfits.
Other than that;
Good luck with the game!