Coz a lot of people who work in the film industry are kind of influenced by the producers... i.e. George Lucas. However, the Creature crew can also kinda enthuse their own ideas upon the producers that this should look this way rather than properly studying and understanding the character properly. I can just imagine what the thought processes were on the TPM Yoda as they redesign Yoda...
"Ok he needsta be Younger but I think we can do a better job than Freeborn did in his day so lets put our own stamp on this guy... I mean we got much better materials now for Gods sake! I wonna see a much better more believable Yoda with more movements and great silicone transculent skin! I mean this is 1999 not 1979!!!"
Thats How I imagine the creature shops crew thought about approaching the TPM Yoda but they really ruined the look and it wasn't Yoda at all but a completely different creature altogether!