mugen's current CNS coding is pretty shit and unprofessional compared to real programming languages, and besides, real programming languages mean we would see higher quality characters and less crappy shinorochievil edits since a higher level of skill would be involved.
As much as I would like to see less crap edits flying around, one of the advertising points of Mugen is that anybody can jump in and learn and all of that shit - making it difficult means that the already somewhat-difficult process of creating a Mugen character will be too much so and be off-putting to would-be creators, leaving almost no new blood within the Mugen community, because it will be so damn hard.
Admittedly, I sorta learned most of what I know by just thinking about it (i.e, what existing Mugen functions and etc., could be used to achieve a certain result, testing them later in x or y character on my computer to see if my logic isn't a load of bullshit), but still - shit's hard as it is, don't make it harder.
Also, a palette changing sctrl means that someone can finally make a Gill that can be thrown correctly, since his flipped sprites are palette swaps of his normal ones, entirely eliminating the need to code them separately and instead use the palette swap sctrl in each state.