I never had a problem with the majority of aliens encountered thus far are humanoid. It does suggest a certain commonality, be it of natural or deliberate design.
I think with TNG there was a conscious effort to move away from having "alien monsters"--be it a guy in a bug-eyed rubber costume or puppets--in order for it to be taken more seriously. There have been a few here and there since then via CGI, but that's one of the more expensive and time-consuming special effects to produce, even more so if you want it to not
look CGI. It's definitely not something a weekly TV show, even one with a decent-sized budget like Trek, can do very often and look good alongside human actors, IMO.
Maybe it's time to go back to guys in rubber suits and puppets if we want more non-humanoid aliens, with CGI aliens every once in a blue moon...