Upvote:3
probably opinion based.
First, I disagree strongly with your statement to book hotels through agencies - they are slightly more expensive (than booking through each hotel's chain website), and often mess things up, don't allow you to change, etc. My experiences are pretty negative, one time the hotel didn't even know about the my 'confirmed' booking and was full - the agency ignored my requests.
For Car Rentals, my experience is the same. Booking through their websites works smooth and easy, and there are never issues. Free cancellation, no prepayment, and better prices.
Your mileage may vary...
[for context: I book about 30 rental cars a year, and about 60 hotel nights]