Seems there's a few elephants in the room here in this discussion. This may sound cynical but reading what's here I'd like to put my few cents in as well.
I'm all for taking .egm into the future with regards to breaking compatibility here and there so long as one can transfer the bulk of say, a GMK project and get it working with some alterations. GM8.x to GMS wasn't a painless process either and with features like BGUI it'd yield additional functionality without stupid sandbox restrictions. I was initially concerned about DLL compatibility with audio engines but looking closer with what ENIGMA provides there isn't that much of a need to use one, it's very functional as it is and much more so than legacy Game Maker.
As for GM compatibility in general, let's not pretend it ever really was the limelight goal of ENIGMA to make a complete stupidity-included GM clone. LateralGM maybe, but not ENIGMA. The potential *is* here to make a game creation engine inspired by GM's environment, but the biggest barriers that remain to bar people from taking serious interest in this project is not the compatibility (that's no.2) but actually getting the f**king IDE to work. Random crashes every 20 minutes, crashes when you press a button after doing a few compiles, modifying folder names to get it to start, modifying commandline arguments, having different versions of Java, error messages that give you no damn clue as to where things went wrong, etc all get in the way of providing a painless experience that both Mark Overmar's Game Maker and the new YoYo/PlayTech Game Maker provides. This combined with the licensing shenanigans is what's holding up adoption of the project.
Compatibility *was* a big deal once upon a time, when simple projects like my Warbird wouldn't behave because object inheritance and alarms were completely unsupported and graphical pipeline changes meant a build one week would display fine and next week have a big black triangle covering half of it and display everything in the wrong shade of colour. That stuff last I checked is long gone, with some of the remaining issues fixed I see has been listed in this very thread!
I feel the remaining barrier to compatibility here at this point (with exception given to unsupported functions that are also unsupported in GM:Studio) is exclusively ENIGMA's parser. The same parser that decided GMOSSE wasn't going to work because apparently the alarms I coded in GM8.0 aren't the same alarms it supports, because I did something slightly unusual in some Draw event and it panicked, because I don't even know what thanks to the completely useless error messages. Perhaps a strip-down of said parser as TheExDeus suggested may actually be a good thing to work towards this end-goal, start from scratch and build up as you say, have a fork of it for certain purposes and someone else can do another fork for GM-specific support, I don't know. Doesn't seem like anyone wants to touch the parser in its current state and I have next to zero C++ knowledge compared to my GML knowledge.