Nah. You do what you can with the budget you have, the restrictions of the mediums you're working with and the time you have to get it done.
In some cases all it really would have taken would have been a piece of dialog. If (for example) they had consistently referred to Mister Sulu as being an alien, coming from a non-Human species, he would have been. Might have explained the blue eyelids too.
They should have created a little bit more variety in aliens. Different skin tones, more monstrous looking by human standards.
I've thought that they could have done more simply by hiring actors/actresses who were not of standard body size. Painfully thin, or unusually tall, or huge bulky people, hire children to depict alien adults.
A prosthetic under the starfleet costume to present spinal ridges (or three breasts) wouldn't have to stand up to close examination.