If you are going to create a new site in this space it has to be at least as good as Kayak. Tripeedo fails horribly. As others have mentioned, a site that simply opens numerous windows with the results from each site is not adequate.
(1) It can help you search discount airlines like JetBlue and Southwest.
(2) It will show you fairs that are exclusive to the airlines' websites. (I don't think I've ever run into a situation where the airline's website had a price significantly lower than what was on Kayak but I've heard rumblings that it happens.)
i recently went to hong kong and searched all of these engines and got discouraging prices. I did one search on Cathay Pacific's website and saved close to 40%. I'm almost positive you won't see this with domestic flights (for now.)
You also provided the evidence of this yourself - I too have had a lot of trouble with Kayak recently, and it seems their ability to scrape accurate fares is severely compromised, and I suspect that airlines have some hand in this.