Of course popularity and commerce will harm the artistic elements. Look at Hollywood example and the huge focus on films for 'mindless Friday night popcorn entertainment' vs films for stimulation of the mind and the senses.
But that's okay. That's just the way it is. The market for more artistic, risky titles will be there - as every it will just need to find the right way to market.
Look at The Last Guardian - the very fact a title like that exists comforts me there will be room for Art as well as commerce.
Also, just like the film industry, sooner or later there's the slump when the well is dry for the latest franchise entry or use of a familiar setting, sales disappoint, and new material is given a chance to flourish.
In the end there probably are more people looking for simple entertainment vs something more challenging, and so long as they and those of us looking for a something a little bit deeper both get enough material then things are fine. I'd hate to deny a lot of people their fun.
Try to be reasonable... its easier than you think...
