The way the maps are laid out is identical to the original, yes, but the 3D graphics don't match for the most part. Also things in the remake were looking way too advanced and still functional rather then the original which was far more primitive, ruinous and dilapidated, successfully showing us a long-since abandoned world. The doors that you destroy in the original game is just once cited example of this change in the remake (not including the unnecessary Ridly fight at the end). AM2R was far closer to the original in terms of design. And despite adding a whole shwack of new things they managed to keep ruinous look intact, and the graphics themselves were awesome to look at.
I totally agree with SR388 being an operational planet, seeming out of place. I get why that non-primitive aspect would totally grate with a Metroid fan. However, that’s really more of a lore or utilitarian aspect narrated by physical interaction, as opposed to ‘level design’, specifically. Let’s call them ‘environments’ vs levels, for the sake of argument.
I agree that in terms of environments (illustrating both narrative and aesthetic) a functional planet, presented cleanly and crisply, with running water, brimming with organic life etc doesn’t suit the context of Metroid II’s events. Although I like the idea of having a ruined planet and reactivating the chozo warps, as chozo ruins, artefacts and technology appear to survive all but a planet’s destruction.
Tbh Nintendo does these little shits and bits in new releases (like they did with Zelda MM 3d, with deleting the Triforce symbology from certain parts of the game, specifically Stone Tower) which if I am hung up on the source material, does bother me to an extent. However, in this case, I believe the choices were to do with efficiency and cost-saving, since they went completely 3D anyway.