The key problem with the reference design card is that the high temperature it runs at leads to instability in the core clocks. It gets so hot that the core clock ends up spiking downwards (sometimes by hundreds of MHz) to keep things under the 95 degree Celsius temperature target. Plus of course there's also the fact it's very noisy, which depending on your sensitivity to this issue, can be a very big problem.
I wouldn't personally recommend getting the ASUS non reference design though. ASUS cheaped out sadly, and just reused the cooler from the nVidia 780 and 780ti. This is a problem because the GPU chip itself in the 780 and 780 ti is noticeably larger in surface area than that in the R9-290. When the cooler is mounted on the R9-290, some of the heat pipes don't actually make contact with the GPU which leads to poor cooling, especially when in a case
(
Source - Yes this is for the 290X, but the chip and the cooler are the same, so the results are still useful. The ASUS example was the hottest when tested inside a case, and had the highest VRM temperature as well. It was also one of the louder ones tested, so the high temperatures weren't due to the fan being run too slowly).
If I was going to buy a R9-290 myself, it would be one of the other non-reference designs, like the MSI Gaming, or the Sapphire Tri-X or the new Sapphire vapor chamber one.