Stripe Atlas is awesome for C corps, which is great if you plan to raise outside capital. If you plan to bootstrap, you're better off creating an LLC in your home state. Atlas only offers LLC's in Delaware.
Why not set up a Delaware LLC? Makes sense if you're doing business online
Unless you live and work in Delaware, you will foreign qualify in another state. You pay taxes to the states you operate in, so if you e.g. register in Delaware and operate in California, you'll be stuck paying both CA ($800) and DE ($400) taxes.
I think Delaware allows “anonymous” llc which not a lot of states do. That is the main draw iirc.