I am the lead developer of Alien Arena http://red.planetarena.org
I looked at Dragonlord's project, and it looks like there is a great start, which makes it all that much more confusing as to why this argument is taking place. He seems to have the ability to make the kind of engine he wants, so there is no need to lament others for not doing so.
Our engine, much like many other engines is being developed for a specific game, and we are a very small team of four, so we don't have the resources/time to worry about making things easier for others to use our engine. As it stands, I've already posted that the only tools you need to work with it are Blender, Gimp, Radiant, and a sound editor. So there isn't really a need for us to create new tools when there are already free ones in place to use(though we did make a radiant of our own for the game). Other than basic physics, most of the flexiblity would come from the game code(meaning you can really make it do most anything). As I stated before, there have been a number of interesting projects created from id Tech that isn't FPS(UFO AI for example).