There's a huge difference between what the clone MMOs copy from WoW and WoW's raid content. Most just copy the user-friendliness of the UI and questing system. It kinda ends there, really.
I can understand the thing about dev time and limitations of FFXI's game engine. You can't do Heigan the Unclean's encounter in FFXI because player movement is very limited. Flame Leviathan would be impossible seeing that there are no vehicle mechanics in FFXI as well. You could probably do a mimic of C'thun from AQ40, provided you have safeguards in place to keep players from dying due to lag at the beginning of the phase inside the stomach (since C'thun's stomach acid deals nature damage to you the whole time you're there). Yogg-saron would probably work too...well, barring the tentacles since the game engine doesn't support multi-targetting. No Malygos because of lack of vehicle mechanics (not to mention the jump button is used during the encounter to control the floating platforms), and lag would be killer on a copy of the Lich King encounter (I can see people missing Quake during phase transitions due to lag and falling to their deaths). Sarth 3D would probably work, provided damage is tuned to allow the tank to actually survive damage to allow the healers to heal the alliance (as Sarth 3D is basically 3 tanks and the whole raid tanking damage at the same time).
Damn it, Aku. You're making me miss WoW raiding. >:O