Being an experienced metroid player, you'll probably want to put it on hard mode from the start, although you can switch at any time.
Also make sure you get the newly released Definitive Edition, which has some extra stuff in it.
You need to know going in that Hyper Metroid is tuned to provide an enjoyable experience for the veteran Super Metroid player, and in absolute terms is thus very hard. In Super, you can facetank everything and spam missiles and get by just fine. Attempting the same method in Hyper will net you only frustration.
To progress, you'll need to be able to get the most out of Samus's mobility, and you'll need to know what techniques to use when, including stuff like the mockball that requires frame-accurate timing and is arguably an engine glitch. If this isn't something with which you have practice, you'll probably do well to work your way up through Project Base (https://a.cocaine.ninja/zicwwx.SMC), on which Hyper is built; they share the same mobility mechanics, but Project Base is otherwise almost entirely vanilla, and will provide a much gentler experience overall as you develop the skills you'll need to progress through Hyper Metroid without finding it overly frustrating.
Hope this helps!
mockballing does allow a big sequence break though, which I guess is what you assumed was the intended route.
Thanks for the heads-up!
http://www.hyper.metroidconstruction.com/