I tend to be a broken record on this subject, but part of the problem is our notion of "species". Hand-authored bots of the same "species" only respect one another (presenting the illusion of a species) because they are coded to do so, but in reality, they are not a species in the sense that we use that term for sexually reproducing organisms, even on the first cycle when they all have the same exact genome. Recognition of likeness for the purposes of reproduction is meaningless in asexually reproducing populations. There is no gene flow between them except for direct line of descent. It's little wonder that hand-coded bots in an evo sim go cannibalistic in short order. Selection favors this since it conveys such a huge advantage to the first bot to violate the fragile and artificial (from selections point of view) conspec code.
In evo sims, after a while, what appears to be a single species is in fact several (or better yet, hundreds) as the hand-coded conspec code breaks down and new systems evolve. In an asexually reproducing population, the whole notion of species is suspect and may not even be relevant. Sure, it helps to be able to recognize your offspring and not eat them, but families do not tend to group or otherwise remain in proximity and there are much easier ways for selection to avoid eating your young than conspec code. One common way is simply not to eat (or not to be very effective at eating) heterotrophs at all. There is no need for conspec recognition at all in a population of asexually reproducing herbivores. All that is necessary is autotroph recognition and even then, it need not be explicit. It could be as simple as just being a really really bad feeder when it comes to feeding upon others of similar genomes. You may try to shoot or tie feed off your offspring or parents, but because you are so ineffective at it (they have slime or shell or similar) at least when you try it against others of similar genomes, the only things you end up really feeding off of are dumb plants.
Our genomes are too simplistic, our sims too small, our environments too simple. There is little need for coordination between individuals and thus little reason for a bot to recognize others it might be related to as long as there is some mechanism at work, no matter how crude (like being a bad feeder) that serves to favor others of similar genomes.
So, in most evo sims, I suspect there is more diversity then one might expect. I have seen larger sims maintain independent families or "lines of descent" (a better term IMHO than "species" in asexually reproducing populations) for 100's of thousands of cycles.
You might try forking the species (use the Make New Species option) occasionally starting with the "Best Bot" and see how long the different families co-exist. Family lines will eventually die out at some point as they get competed, even if families do not directly prey on one another, but you might find this takes much longer than you think. These different families, while they co-exist, can be thought of as different species if you like since there is no gene flow between lines of descent (absent viruses).
FYI, I will likely automate species forking in a coming version.