If you look back they had a lot of good work done on an engine that was similar to Gldsource, but it seems like they saw a new engine they wanted to make it on so they waited for that engine to come out, and that engine came out later than they wanted, then they needed to learn that engine and learn its capabilities. I think that if they released it back on the engine that looked similar to Gldsource they could of made a newer game on a newer engine. The bottom line is they took to much time waiting and not enough time producing.
I read an interview about how Konami and Kojima Productions was going to wait for the PS3 to release before they made Metal Gear Solid 3, as Sony told them it would be out very soon, when it got delayed and delayed they went ahead and made it on the PS2, then put MGS4 out on the PS3, instead of waiting for this new engine they just used the older one to get the product out there, thats what 3D Realms shoulda done.