Just like AM2R's New Game Plus, removes all the progress-blocking lava up to before the the area of the last Alpha and first Omega. Basically nonlinear M2.
How did I do it? Modified transition scripts to load lava-less rooms where applicable, as well as the Metroids remaining check that sets off the earthquake sounds. I also made the Metroids in area count accommodate every Metroid before said area, for technical reasons (it's a linear array of bytes).

Also I was conflicted on whether to submit this a a resource or hack, but ultimately decided hack since it changes progression in the context of the vanilla game (i.e. a full level design hack probably wouldn't rely on the base game's Metroid progression).

UPDATE HISTORY:
v1.0 (2021-03-29) - Initial release.
v1.01 (2021-03-29) - Made a minor level design change (2 tiles) to prevent softlocking if heading to Area 2 without Bombs or Spider Ball (thanks to RT-55J for pointing this out).