Appearance is part of it, but shelf-stability is HUGE. Heirloom tomatoes for instance are so delicate; even if they survive harvest and transport (challenging enough when done by hand, even more so if automated) they can easily get damaged during shelving, customer handling, checkout and bagging, transport home, placement on a counter... More often than not by the time the consumer actually goes to eat it the tomato is covered in bruises and splits (and if the injuries are more than a day old, very likely mold as well). That creates a lose-lose scenario where the customer feels ripped off because their (usually very expensive!) produce went bad before they could eat it, leading to the producers likely losing future business from said unhappy customer.

I think the article hits the nail on the head: this new line of jalapenos is great for processors and therefore will almost certainly stick around, so it's important for other consumers to demand labeling of new vs more traditional jalapenos and the stocking of both at suppliers and grocery stores. Going back to the tomato example, I love heirlooms but still buy more recently-bred tomatoes for certain uses (e.g. a recipe I won't be making for a few days). Plus tomatoes wouldn't be available year-round had not varieties that handle transport and storage better been developed.

As always, for the best quality produce the ranking goes: grow it yourself > buy it direct from a farmer > buy it from a retailer that sources locally > buy it from a retailer that does not source locally.