The fun part of ATL Native American development is that we can very reasonably postulate some ATL crop that is nonexistent or nearly so OTL. Against this, we have to educate ourselves about botany to arrive at a plausible crop, and then ask "how come they didn't develop it OTL?" The fact we are working with which is a double edged sword is that Native Americans in both continents were very forthcoming with numerous crops, indeed aspects of the grander ecosystem (such as a rich variety of nut and fruit trees in North America, and a similar abundance of useful plants growing wild today in Amazonia) appear to have been enhanced by Native practices, some of them known but discounted in their importance to European invaders. Thus we might say low intensity, extensive, quite profitable cultivation of entire ecosystems that appeared to Europeans to be pristine wilderness was a widespread practice in America. It is well known native North Americans set fires which we now understand had the effect of making the landscape much more hospitable to gathering and hunting--also, once US and other authorities asserted themselves and banned these practices, the danger of wild fires grew; Native management by widespread but somewhat controlled burns was important in that respect too.
So the double edged sword is that Native Americans did put a lot of effort into developing cultivars, so we might be skeptical in proposing some unknown to OTL variant since we could reasonably ask, mustn't there be some impediment or they'd have developed it OTL? Against that, relatively few regions (though these regions no doubt tended to account for a substantial percentage of the 1491 net population, which is a matter of great controversy in its reconstruction) became intensively cultivated; most populations were low in density with a mixed gatherer-hunter/cultivation set of practices and a high degree of population mobility. Again we are probably underestimating the total effort put in to cultivation in the broadest senses, such as North American controlled burn fires, and thus overestimating the "natural" ecosystem's bounty without such manipulations. But the relevant thing here is that populations were not generally up against a hard Malthusian wall to grind out as much productivity as they could to avoid starvation, they were often closer to gatherer-hunter densities where a hard year for the crops just means switching to more intensive gathering and hunting, with the population to be sustained reasonably small enough to survive that way.
Therefore the way it looks to me is that something peculiar about Native American cultivation is that they seem to have had quite a good skill set for identifying and improving a wide diversity of crops, without too much pressure to perfect many of them--in a few places such as the Andes re potatoes, or MesoAmerica re maize and the other "sisters" (beans, squash, peppers, tomatoes) they did get fully onto the "civilization" on-ramp and I believe therefore famine was more often a thing among them--putting more pressure on maintaining crop diversity I would think.
Against that--part of our evidence of a general American Native propensity to come up with diverse crops is the sequence in which spreading "sisters" from MesoAmerica being adapted for more and more northerly climes resulted in certain other crops already in cultivation in areas the maize et al spread into being abandoned.
But that brings us back to the general diversity and plain activity of humans improving cultivars quite a lot. Overall it seems plausible that one can pick just about any ecosystem at random and examine it for a potential crop, and then plausibly decree a POD in which some people does develop this crop, and extrapolate higher population densities and at some critical point, a civilization where such development was unknown OTL.
The Mississippi region thus had other crops prior to the spread of maize and its "sisters." An ATL crop that stands its ground, or perhaps best of all is mixed with the spreading Sisters, and perhaps itself spreads both north and south, to enrich at least parts of Mesoamerica and perhaps prove adaptable in the Caribbean, while giving an even earlier and denser population in some selected core region and spreading periphery where the ATL crop, probably forming a suite of many such, some known to OTL but more developed, others being completely unknown, form a big part of it for high population density, is something we can reasonably suggest, provided we do our botanical homework anyway. We might ask, what unique constraints on Sisters or OTL predecessor crops does some select part of the Mississippi system impose--high humidity favoring blight molds perhaps, variable rainfall being a challenge, snap frosts blasting all the way or most of the way down to the Gulf of Mexico from the vast North American winter cold basin--might some ATL variety of something be superior at handling, and thus favored, and raising the general carrying capacity?
Are we interested in the near-tropical lower reaches in OTL states of Louisiana and Mississippi, perhaps with an eye toward fostering a maritime civilization based out of coastal bayous, and perhaps therefore some cultivar that grows in these swamps?
Are we more interested in the upper river and its numerous branches, with any enhanced Bayou civilization being fostered by down-river trade? The Great Lakes being its own lake-thallasocracy region maybe? I'm especially interested in a system that takes to a lot of boat-borne commerce since it would tend to spread far and wide and find lots of little enclaves in regions generally forbidding, and from those enclaves spread out new crop adaptions more suited to the general region, thus maximizing the development of cultivation in the continent--and perhaps both, if trade reaches from OTL US Gulf coast to Venezuela and Colombia and perhaps beyond. Might Amazonian cultivation methods, known by now to have existed, have spread to other rain forest areas deemed "nonproductive" OTL to present the Europeans with even more worlds to conquer?
I do think no matter how many extra civilizations we conjure up, all of them will collapse pretty catastrophically after 1500. The more developed and populous they are, the more damage Old World diseases will do. I am aware many argue that the staggering degree of OTL collapse related to the Europeans following up on the wavefronts of suddenly stricken populations and presenting them with war, conquest, religious persecution and enserfment which caused the collapse to accelerate, and if there are more civilizations to divert Conquistador and other European colonization fronts, it may take a while for this wave front of sweeping conquest to reach various heartlands, buying time for some targeted centers to recover better.
I don't know though. There wasn't much effort on the part of either Spain or Portugal to follow up the initial probes up the Amazon system to batten chains on the surviving Terra Prieta cultivation centers for God and Profit, the one intrusion by explorers whose accounts were subsequently discounted as fantastic fabrication seems to have been enough to so collapse those populations the surviving peoples abandoned such cultivation and lived on a mix of gathering and hunting and very marginal jungle floor cultivation.
Similarly, if we don't think the OTL Mississippian development was quite grand enough, we should remember De Soto observed quite a lot more in the way of civilization than later explorers and pioneers did--because again the single expedition clearly was culpable for massive die-back, in this case apparently largely from European pigs the Spanish had in their entourage getting loose, going feral in the North American wilds, and spreading European diseases endemic to themselves into various Native American wildlife from which it then afflicted populations that never came near De Soto's own men. It is a sad story quite similar to Amazonia; the difference would be if we could demonstrate say 4-10 times population density and a lot more in the way of massive mound works and perhaps stone buildings (but of course, timber would be favored regionally) littering the landscape, the invader Europeans would presumably find 1) somewhat more Native people, some of whom might be pretty deeply committed to cultivation--as a target of missionaries, they'd quite likely even be somewhat Europeanized, converts at least nominally to Catholicism or some Protestant denomination and 2) a huge Ozymandian array of evident earthworks and perhaps other monumental displays of a once mighty civilization complex, perhaps with writing either derived from MesoAmerican or perhaps as likely or likelier, independently invented, with forms of this writing scattered among otherwise not very dense or cultivation intense Native American peoples. Again a North American complex east of the Rockies (or on the Pacific coast for that matter) would be likely to build in materials tending to fall into obscurity, such as wood, but the sheer number of such remnants, and the probability that at least a few are really massive complexes of really ambitious structures, should not fail to impress.
To be sure, OTL pioneers wrote off the possibility the Native peoples they faced had anything to do with these great works and dreamed up all sorts of ideas, of ancient Egyptian or Atlantean colonies or various Biblical notions (lost tribes of Israel being popular) and even with ten or twenty times more earthworks and some enclaves of Native peoples who continue to practice forms of the old cultivation and demonstrate some retained "civilization" of their own, it might be possible for this dismissal to be the popular theory among the pioneers. Eventually scholars will face up to the evidence it was all Native work, but not while the claim of invading European settlers is in doubt I think.
