The biggest challenge facing the segment is innovation. Everything is exactly the same over the last decade!
It's hard to differentiate yourself in this segment.
There is one other pain point though -- sanitization of the networks feeds. All the networks should create an industry standard way of doing merchant feeds and ensure merchants populate their feeds properly. This was a huge pain when I was creating a price comparison engine back in 2002 -- and the issue still exists today in 2014!