I would need to see more data before I would accept the blame the queens argument. I would argue that disease tolerant traits can be selected for in productive lines of bees without sacrificing any economically valuable traits.
Nutrition and mites seem to be the main culprits in most struggling apiaries. On the nutrition front, loss of forage due to large scale Roundup ready style monoculture means a lot less variety in bee diet. Oliver's article in this months ABJ addresses this.