I think it would be a good time to summarize the answers from repliers I have received, which I appreciate, when the answered why the series after the first 3-series. Plus my quick thoughts on the answers, I do not think I missed any, It is going to be very general, not as detailed some might want.
Cost of doing non-humanoid shape aliens, but since we talking advancing technologies after ‘The Next Generation’ lowering costs & series like the very next series in ‘Deep Space Nine’ starting-existing on new & cheap networks, like ‘Deep Space Nine’s starting on ‘Paramount’ owned ‘Viacom’ & rest of existence on ‘UPN’. These networks are NOT going to spend money & resources on the series, even if they brought it about, if they are NOT getting the audience ratings. Wait, wait & wait a sec. here I have add a huge addition to my above comments, cannot believe I did not think of this first-time, The Networks will also cancel or put a lot pressure on programming that not fit their politics-political messaging. Network censorship caused?
Time it takes to do that effects to have non-humanoid shaped aliens, but again advancing technologies lowers the time factor as well & depends upon what networks are willing to accept.
Complexity of communicating with rest of crew & Etc., but I think of the movie ‘Contact’ solving the very problem. Plus they all have universal translators,
Complexity of manipulating the machines involved in the space travel, but ‘Star Trek’ series like ‘Enterprise’ already have had aliens that are not able to traditionally, by our biases, manipulate the machines are still able to manipulate the machines. Example of ‘Enterprise’ has regular aliens that can only live in liquid/water. The original series had aliens that did not even need spaceships, let alone manipulating machines.
There were series that have had non-Humanoid Shaped aliens, but they are few & far between or not important characters or that last past a episode or two.
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Last one, I am going to introduce myself, because I have the feeling that some repliers believe it is at least a factor- SciFi audience is not ready to not see themselves/humanoid shaped in almost every single Being in a ‘Star Trek’ series. My response is simple & equally serious, I have a lot more faith in The SciFi & ‘Star Trek’ audiences. I think they would not only accept at least some of the characters, especially some main characters, being of non-Humanoid Shaped, but they would love it & reward the series that does it.