As an ex - videogame developer I've shipped several titles from simple 'kids' games to AAA titles. Here's my take:
You CAN make good looking games on an indie budget. Plenty of indie developers do it. However this requires an Artistic Director which oversees the visual style and coherence for the game.
Some programmers (very few I know) have both technical talent and have a very good 'eye' artistically. They are able to make games and make them look good. It's once again still about style and visual coherence.
Obviously the writer of the post is not an artist so he might not necessarily have the time or inclination to dwell on such visual coherence and direction. That's fine, he accepts that.
But I can't agree with the fact that being and indie makes it harder to have a pleasing visual aesthetic. That is simply a question of choice, which you can rationalize with any type of arguments.
That being said I'm really impressed with their success and hope them all the best for the next 25 years!