Given my understanding of how FSO works (which is not tremendous), I fully agree with portej's sentiments.
Took the words right out of my mouth. I've never been a coder in anything beyond some PHP, but every time I've encountered a program of some sort that stores its data in external, human-readable files, such as .ini or .xml files, it makes it that much easier to start tweaking things to work the way
I want them to.
Pardon me while I wax poetic for a bit.

Taking a step back, we can see how :V:'s decisions in the past have had a tremendous effect on the present. Think about it. Freespace 2 is 11 years old. Why do we even exist? Back in the days before the source code was released, things were lively primarily due to 2 tools: FRED and PCS. With them, we could write our own stories, and paint our own pictures. If we had not been able to modify things, to create new content, everything would have stagnated after the 2nd or 3rd playthrough, and :V: would never have bothered releasing the source code to a non-existent community.
To keep things alive, we need to have those abilities for storytelling and art creation. FSO could be enhanced to become the bestest game engine ever made for the next 100 years, and without the tools to do anything with it, it wouldn't be used. I realize that some of the SCP coders probably are coding for the fun of it... they simply enjoy coding, they enjoy the rush of success they get when a feature they created from scratch starts to work properly. But keep in mind that there are hordes of FREDders, modelers, texturers, writers, and modders who need the right tools to be able to do things with what the coders create. Think of it as a Buggati Veyron in the midst of craggy, snow-covered mountains. It's a marvel of engineering and design, framed in majestic vistas, but without a road to drive on, it's pretty much useless.
I used to dabble a lot in FRED and modelling. I stopped when I saw that the tools weren't keeping up with the engine.

[/poetic_waxage]
Think over what portej05 said about a feature freeze for the sake of a complete overhaul and documentation. Even with the mantra of retail compatibility, it can't be impossible. Netbooks prove that - things had gotten so fast, that instead of making them faster and better, people went for just sufficient performance using the admirable efficiency of today's technology. So it seems to me that the engine could be completely overhauled, with retail compatibility replaced by meta-data support, and we'd still be left with processing power on today's rigs to run an "external" abstraction engine for retail-compatible data.