Thank you! I'll let you know how it goes. The guys at Doom Reborn asked for a hand with getting the Doomsday models into their mod.
I was talking to gamehacker over at Doom Reborn and we are both wondering if the lack of exporters for MD5 is part of the reason why the modding community has pretty much dried up.
I already imported animated md5 models into Doom 3 successfully, albait basic ones not full characters, using the Arx team exporter and i already explained above how i did it, but again, you just need to remember, one name the first bone "origin", two put the bones you want to export into blender layer 5, this is a requirement, this means the basic armature not the complex rig with all the control bones, shapes and modifiers, four be careful with weight painting the mesh, sometimes you think you have all bones perfectly weighted but they are not, happened to me.
Like The Happy Frier said the exporters are made in accordance to the workflow of the team that made it so if you work in a different style you will certainly find problems, we just need to adapt to it.
Learning a 3D program is a PITA and players are super-critical of any releases compared to the 90's. A lot of negativity a modder has to put up with if they want to release something now a days.
That is true but is not why the idtech 4 modding scene is this small, the truth imo is because idtech 4 based games were not very successful, enough to amass a big following, one willing to spend time learning the tools, specially when everyone now wants a "press a button" for game, kind of tools plus the engine market imploded, making AAA engines like UE4, Cryengine, etc become cheap to use, everyone and their mother flocked to them to make the "game of their dreams".
Alternatively if fhDOOM will get tools back, maybe I'll use fhDOOM 
fhDoom has all the tools including a improved light editor.