There are lots of reasons why Nintendo filed a lawsuit and not "just a DMCA takedown request".

Nintendo didn't just use a DMCA takedown request because those apply to user generated content on a public repository of data. See: YouTube videos, Soundcloud uploads, GitHub repositories, etc. Those are selective content objections filed to site operators that a license holder asks for removal/delisting of infringing works.

In this case not only was it Nintendo content, it was the whole site flagrantly abusing IP laws. Had they issued a takedown request, it would have been sent to LoveROM/Retro's web host, domain registrar, etc. But directly contacting the site operators was relevant because I doubt that had a "DMCA claim fulfillment" section of their site. Additionally, it was also delivered as a legal order due to apparent monetization on the infringing data.

yknow a lot of the first friends I made on the internet were all part of the emulation/ROMs community, so I can definitely appreciate the angle they presented for the debate, that we're preserving these games so that future generations can enjoy them and yes, maybe even learn from them!!

I would totally be okay with Nintendo if they were gonna use their legal muscle on these sites, but also that this 'NES-flix' that they're proposing would cover as much of their NES library as they could get the rights to do!

Yeah I'd be okay with skipping say, Color a Dinosaur but surely at least giving us their entire first-party lineup wouldn't be asking too much, would it? At least SEGA's been good about keeping most of their first-party stuff readily available for anyone that wants to play it.