And not design them according to their own appearance?
I mean, otherwise that would mean the Protheans that engineered them had some weird fetishes.
There are more considerations for an alien geneticist designing new races than merely producing the best sex toy for his race.
I believe that in the ME universe the Protheans either made or changed the humans to suit a future role of a client race.
They probably streamlined many races into a relatively similar look: Humans, Asari, Batarians, Drell, Quarians, perhaps even Turians,
and planned for them to fill different roles in their empire.
The Asari were probably meant to fill a higher position or caste within the Prothean system, based on their long life-span, natural biotics,
and their melding ability - that in a way - is somewhat similar to the way Protheans are supposedly able to do psychometry.
The logic behind not making them all look like Protheans is very simple: The Protheans are to remain the "Gods" of their time, the "lesser" races should not look the same as them.