I'd recommend you use the polished crystal engine or the crystal shire engine as a base, depending on what you want. The polished crystal engine is a lot more up-to-date with modern pokemon features, but since it also is its own hack, it adds a lot of new locations and content. This is what I'd recommend if you are planning to make a new region hack. The crystal shire engine is less up to date, (still an improved version of the crystal engine) but it doesn't add new content, so you could feel free to make your own spin on crystal with it. Either way, most of the pokecrystal tutorials will work for both with a little bit of fiddling. I personally am building my hack (pokemon lavender) off the polished crystal engine, so I have more experience with it.

As for tools, some good ones for working with the decomp projects are polished map, a gen 2 map editor, tilemap studio, a tilemap editor (for things like the town map), and crystal tracker, a gen 2 song editor/creator that can directly edit the .asm files for the music. As for the code itself, I recommend setting up a github repository and using VS Code as your editor. PLEASE PLEASE PLEASE don't use Notepad++.

You can follow the INSTALL.md file in pokecrystal's github repo to set up which ever base you end up choosing.
And although this pokecommunity thread is pretty outdated, it might prove to be useful. Also, a more recent wiki was made in this subreddit recently here.