They're not. Again, and a lot of people seem to ignore or forget this, evolution DOES NOT WORK THAT FAST. Not in any species with a time to sexual maturity of decades or longer.
Humans have existed in their current form for three to five MILLION years, and the precursors for longer than that. 50,000 years is barely long enough for Prothean genetic tampering to enable all asari to tap their natural biotic potential without the need for biotic amps.
The idea that somehow the Protheans 'engineered' the Asari into their current form a mere 50k years ago is beyond laughable.
You are right in you assertion about evolution and the protheans but wrong about the facts. You also preclude the possibility that the Protheans didn't just genetically engineer the Asari to how they wanted which would not require Evolutionary time scales.
Hominids have been around between 1.3 and 1.8 million years that is it not 3 to 5 million years and that is the first branch of the evolutionary journey that creates modern humans. we are quite young on the evolutionary scale.
H0mo erectus and H0mo ergaster were the first of the hominina 1.3 to 1.8 million years ago. It is believed that these species were the first to use fire and complex tools.
Modern humans are not that old only 200,000 years or so...
Nomenclature and anatomy
The binomial name for the taxonomic species of the human population is H0mo sapiens. The species is usually taken to have emerged from a predecessor within the H0mo genus around 200,000 years ago.[10][11]
Anatomically modern humans evolved from archaic H0mo sapiens in the Middle Paleolithic, about 200,000 years ago.[3] The emergence of anatomically modern human marks the dawn of the subspecies H0mo sapiens sapiens,[4] i.e. the subspecies of H0mo sapiens that includes all modern humans. The oldest fossil remains of anatomically modern humans are the Omo remains, which date to 195,000 (±5,000) years ago and include two partial skulls as well as arm, leg, foot and pelvis bones.[5][6]
Other fossils include the proposed H0mo sapiens idaltu from Herto in Ethiopia that are almost 160,000 years old[7] and remains from Skhul in Israel that are 90,000 years old.[8] The oldest human fossil from which an entire genome has been extracted belongs to a man who lived about 45,000 years ago in Western Siberia.[9]
Source http://en.wikipedia....y_modern_humans
What's not unreasonable is for protheans to genetically modify a species 50,000 years ago to obtain traits they wanted in the species. These wouldn't be subtle changes the shaped natural evolution but radical changes that replaced the natural evolution of the species. It is not unreasonable for the Protheans to have genetically engineered the Asari to be longer lived and that advantage spread to the entire species in 50,000 years. populations in pre aquarian societies are very small so giving one group this technology as well as mathematics, along with genetically engineering them could result in this one group supplanting the entire "stock" version of the species in said time. The Neaderthals died out only 30,000 years ago. So 50,000 years is within the time frame but this means the protheans had to make radical changes not subtle changes that let natural evolution take its course with a slight push.
H0mo neanderthalensis, which became extinct 30,000 years ago, has sometimes been classified as a subspecies, "H0mo sapiens neanderthalensis";
source http://en.wikipedia....ki/Homo_sapiens
If a group of Protheans gave technological and Genetic advantages to one group of Asari 50,000 years ago it is not outside the time scales we are talking about for this Asari Superious to replace all the Asari naturalis. Having both a genetic and a technological advantage over other Asari would be bad enough but these Asari Superious would also have a numerical advantage as well that an agrarian society has over a hunter gatherer society. Also if these genetic advantages were dominate then they could and would be passed down when the two groups interbreed thus you don't need to conceive of all the "old" asari as dying but rather being breed out as well as natural population reducers that agrarian societies have on hunter gatherer societies which would have eradicated some groups that were on the margins of survival to begin with without any other advantages like we have seen happen here on earth. Agrarian societies in and of themselves can have a devastating effect on hunter gatherer societies when these two groups collide, add in a biological advantage and I think the results could be even more devastating.
Is it beyond the scope of Prothean technology to genetically modify the Asari and to make said alterations genetically dominate? I don't think so.
please excuse using H0mo as using h omo cause the stupid censor to go into overdrive.