Not entirely true - Skyscanner certainly does include budget airlines (in fact, long ago it supported only budget carriers); see below for plenty of easyJet flights between London and Berlin

http://www.skyscanner.net/flights/lond/berl/1302/1302

There are definitely challenges in gathering & displaying a combination of budget and 'traditional' carrier fares, but to say that either set isn't available via flight search isn't accurate