Since these cutscenes are in-engine, isn't it possible to code a texture swap, swap Barrier textures for Gravity textures or something? You're just changing the orange parts of the suit then and the cutscene should still use the Barrier model so hopefully no breakage. Also maybe re-swap the textures back after the cutscene is finished to be safe.
(also, small suggestion IF this can be done; during the flashback on meeting the Baby Metroid on SR388, make Samus have the Gravity Suit in line with Metroid Samus Returns. You could also have Samus in the Gravity Suit in the opening against Mother Brain, but if left unchanged you can easily say the suit was damaged by the Hyper Beam and was shutting down suits.)
Problem with that is that all the other cutscenes which do use barrier's texture would use gravity's now.
I need to find precisely where the game determines what model to load for each cutscene, so I can make the proper change. Making a texture change would break other cutscenes. I'm not sure precisely what cutscene the barrier model starts being used, but I think it's after event dm24 that the Varia Suit is activated.
I tried looking around in the files for any kind of calls for cutscenes but didn't have any luck so far.
About your second suggestion, I did attempt doing that at one point. Isn't the scene with the Baby Metroid in sepia tone though?
As for the Mother Brain one, I did try, but damn the lighting and everything else in the scene makes it obnoxiously hard to work with for masking with video editors.
If someone has a way to change Samus' Varia Suit colours in that one to be Gravity Suit, that'd be amazing, I just couldn't do it with Cyberlink's Color Director, maybe there's a better (and free) tool to make it, but I didn't find one.