I'm not familiar with shady sites, but probably >75% of my previous 50 trips were booked through Kayak or similar sites. They make it painless to group everything you need for where you are going, and if there is any problem, like a flight delay, etc., since it was booked all together, they just adjust the future bookings/book other flights as necessary to make sure your trip is smooth riding. Any time I need more than just one resource (car, hotel, flight), I use a consolidator because if they aren't bundled, no one lifts a finger to help you when anything out of your control happens, but they bend over backwards to help if you used a booking site.
The last consolidator I used (I forget the name, but it was nearly "obviously a shell Amazon company"-level strange) saved me nearly $1000 on three flights and two hotels, but it routed me through seven completely different domains to do it, sometimes with the bulk of the page in an embedded iframe for yet another site. Once it was two layers of iframes deep. I checked because by this point I was flabbergasted by the whole process.
Many pages took tens of seconds to load and had a single field to fill out, broken links to information, etc. I had to fill in my personal info three times, on different pages, with wildly different layouts and misspelled fields. It had to be done over four separate days, because two pages had 503 errors and a couple others told me to wait up to 5 business days for "procesing" or "processin" or other misspellings, though it only turned out to need a couple minutes or hours.
I watched my card for unexpected charges like a maniac as emails from different domains every time came in to inform me that I was still good to go. But the tickets came through fine, about 3 weeks later, less a week before my flight.
From reddit, I'm under the impression that this is a somewhat average experience.