As with potatoes from South America, the major difference is that commercial corn tends to be from a narrower range of cultivars (e.g. plant variants) than were available to Native people. Indeed, the diversity of corn cultivars (or "landraces") historically would be such that we can't really talk about any such thing as "Indian corn" because each group of people would potentially grow quite a different mix of landraces.

Because of this, to answer your question we need to consider the main axes along which maize landraces differed in the past in order to see how they might differ from modern corn as a group. By modern corn I will assume mono-culture corn as it is grown in the U.S.A since there is still quite the diversity of corn cultivars in other parts of the world, particularly is less intensified/industrial farming contexts. I'm also only going to be speaking about corn cultivation in the U.S. Southwest - the situation could be quite different in other corn-growing areas of the Americas, including Central America, the Eastern Woodlands, and the Andes.

To quote from Adams et al. (2006:2):

Landraces can be distinguished from one another on the basis of many traits. Among these are: (a) rates/timing of plant growth and development; (b) plant phenotypic traits (plant height, size of stalks and leaves, etc.); (c) ear size, shape, and number of kernel rows; (d) kernel color, endosperm type, and spacing between kernel rows; (e) average kernel (grain) yield per ear or per plant; (f) moisture and temperature requirements, such as number of frost-free days and accumulated growing season heate units needed to produce mature ears; and (g) day length sensitivity/insensitivity. Traits related to taste, ease of grinding, dependability, and religious/ceremonial requirements may also be important to indigenous conceptions of maize landraces.

As you might notice, these traits largely fall into either morphological/phenotypic differences or differences in environmental requirements and field cycle (e.g. life cycle). In the U.S. Southwest in particular (and I don't discuss other maize-growing regions for this reason) the restrictions of growing a sub-tropical plant (maize) in an arid or semi-arid environment means that a large component in determining the caloric yields of a plant are environmental, including temperature and water most prominently. The drastic changes in elevation across the U.S. Southwest (from ~2000 ft above sea level to around 8,000 ft above sea level, or even higher in some places) as well as highly variable rainfall patterns (from year to year and across the landscape) mean that the tolerances of a particular cultivar for this variability is going to be the primary factor in what kind of yields you will get from the crop. The huge variety of maize cultivars in the U.S. Southwest historically are a response to this environmental variability, since:

The plant's [maize's] potential to produce under particular environmental conditions is a function of its genetic potential

(Adams et al. 2006:6-7)

A lot of this diversity wouldn't necessarily leave a mark on the corn cob itself, being seen only in the field as it grows. That said, many of these crucial traits could be communicated through the physical attributes of the corn. For instance, the huge variety of colors and morphologies in corn cultivars (a sample of which can be seen here) are likely indicators of the other genetic traits of that particular cultivar. For instance, a cultivar with a tolerance for late frosts in the growing season might have a particular color or number of rows of kernels. Ethnohistorically, Pueblo farmers are very cautious to plant different cultivars of corn as far from each other as they can to avoid cross-pollination since that would both potentially dilute the desirable genetic traits of that cultivar and weaken the morphological/phenotypic signals of those desirable traits.

Along these lines, while some of these traits might reduce the caloric yield from a particular plant (smaller cobs for instance, in comparison with the monstrous yellow-corn cobs you find in supermarkets), the trade-off for a smaller cob or fewer kernels might in some cases be a greater resilience to particular environmental factors (short growing season or low rainfall, for instance). Your yield per-plant is in this case much lower, but the ability to grow in areas where a higher-yield cultivar would fail means you are increasing your yield on the landscape in total. For instance, there is some evidence that the earliest corn cultivars in the U.S. Southwest had considerably lower yields than cultivars developed more recently (see Diehl 2005). This may have been a product of selecting for cultivars that could cope with the semi-arid environment of southern Arizona, with the trade-off being a lower yield per plant. Being the earliest corn grown in the area there hadn't been enough time yet to develop cultivars with higher yields but which also had a desirable response to arid-land agriculture.

This isn't much of a concern in modern agriculture since the kind of maize agriculture in the U.S. corn belt is set up to essentially provide the ideal environmental conditions for a high-yield variant. This is going to be the major difference between modern corn cultivars and historic cultivars in the U.S. Southwest:

• Native people manipulated the highly plastic genetics of corn to create a mosaic of cultivars suited to a large range of environments

• Modern maize agriculture is focused more on manipulating the environment to be ideal for a narrow range of high-yield per plant cultivars (thought of course genetic manipulation is still a major component to create the highest yield given our agricultural practices).

I don't address the possible nutritional differences between corn cultivars here, but that is largely because that is not an area with a lot of research to draw from. Archaeological, ethnological, and experimental studies of corn cultivars have largely focused on their field properties and phenotypic/morphological qualities, rather than their nutritional properties.

In short, there is a huge variety of cultivars lumped under the category "Indian corn", some of which may have been very similar to modern variants, but some of which may have been very dissimilar. I would suggest that cultivars used in strategies which replicated ideal growing conditions (i.e. canal irrigation) would be most similar to popular commercial variants (grown through irrigation). For instance, modern Puebloan corn varieties meant to grow in irrigated fields are likely quite similar to the most popular commercial cultivars by virtue of being grown in similar environments. Other cultivars that might have been grown at high elevations or under water regimes quite different from canal irrigation (dune agriculture, for instance) would probably be the cultivars most different from both commercial varieties and irrigated varieties.

Edit: Typos and clarification.

Sources:

• Adams, K. R., Meegan, C. M., Ortman, S. G., Howell, R. E., Werth, L. C., Muenchrath, D. A., ... & Gardner, C. A. (2006). MAIS (Maize of American Indigenous Societies) Southwest: ear descriptions and traits that distinguish 27 morphologically distinct groups of 123 historic USDA maize (Zea mays L. spp. Mays) accessions and data relevant to archaeological subsistence models. Arizona State University, Tempe, Arizona.

• Diehl, M. (2005). Morphological Observations on Recently Recovered Early Agricultural Period Maize Cob Fragments from Southern Arizona. American Antiquity, 70(2), 361-375.