To be honest, I disagree with the idea that it was a mistake. Their design intention was quite clear on the R2: low air flow and near-silent operation at reasonable cost compared to the Antec 180. Whilst modularisation of the HDD bays is a great idea when done well, it costs money in design and manufacture and is relatively hard to do correctly. Similarly extending the length of the case to accommodate 12+ inch cards is possible but would increase cost at a time when buyers were very cost-conscious and bring its' price point perilously close to the P180, which IMO would have been bad news for them as a new company. As it is they've designed a case which will accommodate most of the high-end GFX cards, just not the Dual-GPU monsters. The R3, as it is just a refresh of the R2, isn't the sort of major redesign in which you'd expect to see it addressed and stay at roughly the same price.
I would level the criticism at the CM690-II however. It's obviously intended to be a performance chassis with high air-flow and cooling, but by all accounts space for 12inch cards was removed in the update from the CM690. In addition Coolermaster isn't exactly new to this game and don't have the brand weaknesses that would bring.