I originally leaned towards including the Protheans, maybe more were found. The green biotics would be fun to see squadmates using too.
I was thinking just now that Sur'Kesh would take decades to clone and raise new Protheans, making that explanation a weak one. Also I think the novelty of using Protheans would be lost on us in just a few weeks to perhaps a couple of months.
What's beautiful about their story is that the Protheans are doomed, Commander Javik is the last voice of an inevitable extinction, and having more Protheans diminishes his plight, our sympathy for him, and for the more emotionally involved, sharing his seething rage for vengeance.
If all of humanity was destroyed by the Reapers and you were the only one left, no hope for your race's survival, would you want to crush every living Reaper? And what if you found there were 100 other humans still alive? It gives you hope. Commander Javik is great, one reason being he has no hope of this happening.
"The last Prothean has spoken."