Well, I 'blew' that ID. Yes, it is A. nijsseni. The difference between nijsseni & panduro are easy to see, especially on females. Male nijsseni: small caudal spot that does not extend into the base of the caudal fin and all dorsal spines even. Male panduro: larger caudal spot that extends into caudal fin and first dorsal spines slightly longer than others. Female nijsseni: cheek entirely covered in black pigment and large black oval flank patch (panda markings). Female panduro: cheek stripe or only part of gill cover black and either a broad vertical band or black patch on the lower abdomin.
I think you are asking why species are different and not how they are different. If so, the why is due to isolation in time and location. All related species once had one ancestor in common (monophylly). When this one species spreads to new locations, many locations become physically cut off from the rest of the common gene pool and any mutations in their genetics cannot be passed on to other populations. Over time most of these isolated populations develop traits different from the original - and other - populations that arose from the original species (evolution). These traits can be so different that populations that once were one species and could interbreed are now unable to do so. So where we once had one species we now have several.
Several years ago I wrote a l-o-n-n-n-g article that discusses the how as it relates to the evolution and distribution of apisto species-groups. It needs some updating now. If you are willing to wade through it you can find it at Tom C's website: http://www.tomc.no/page.aspx?PageId=119.
I think I understand the why but i actually do mean the how - are some more aggressive for example? Prefer warmer waters? Spawn in cave or spawn on substrate. WIll work as a team to raise the frys. You mentioned the wolli for example as being harder to breed. Why is it more difficult to breed? I only have three species (or is it subspecies) of apistogramma. None are wild (intentional) and none of attempt to breed yet (most were purchased at 1/4 or 1/2 inch and I have been growing them out - though the apistogramma cacatuoides are close. So far I find nothing exceptional about the cacatuoides other than being a pretty face and that is in itself so so. I find the kribs behavior somewhat amusing (not only in how they raise the frys but in how they have adapted in treating the other fishes over time - for example initally they brutalized the pygmy cory but now they no longer see them as either threat or intruder and leave them alone - even allowing them to feed along (or at least very close) to the frys.
I mean when we discuss a specific subspecies it would be include to indicate what makes it unique or different than another.
From what I read (and maybe I'm wrong; not the first time) it appears that your understanding of biology and evolution are a bit lacking. For example, scientifically there are no sub-species of apistogramma anymore. You either have different species that belong to the genus Apistogramma or possibly different color strains of the same species. What makes a fish "exceptional" depends on the hobbyist. For example, I prefer wild forms more than domestic color strains. That's just me; one is no more exceptional than the other overall. Also realize that Kribs and apistos are very different fish with very different behavior patterns.
Behavior is an attribute of evolution. Some species live in areas where aggression, for example, is a survival mechanism that species in other areas don't need and have to a lesser extent. An excellent example is A. steindachneri in the wild. In areas with low numbers of fry predators males tend to be more polygamous. In areas where there are more predators the males are monogamous and join the female in protecting fry. This is a behavioral survival mechanism. Will this affect their future evolution physically (increased size, more ornate males to distract predators from fry/females)? Possibly.
The detail that you are asking for is more than can be discussed here. There are many books that discuss these topics, in general and for individual species. I suggest you look for books by Ingo Koslowski or Uwe Römer. These authors go into these topics in more detail.