I bought a house a few years ago. Tried two realtor's through USAA's service where they provide a cash-back based on the purchase price (by taking it from the selling agent's commission). Those realtor's felt like they weren't listening, were trying to get me to just buy something, and wanted to turn things around ASAP. Could have been coincidence, but they were also working for a large well-known firm.
Got a referral to an independent realtor who owned her own small company and she verbally agreed to match USAA's discount. She provided good service. After a couple weekends of looking at houses she had a good idea of what I was looking for and was able to see things go on the market and *correctly* determine that I would like it and let me know. She was able to save me and her much time because she was able to put herself in my head (neither of the previous realtors bothered to really listen so couldn't do that)... and was able to point out issues that me, not having owned a house before, wouldn't have known what to look for. There were a few houses that I initially liked but she pointed out issues with and scuttled any chance of me purchasing.
That said, despite me taking a few months before I found the place I was happy with she didn't ever make me feel pressured or hurried.
I was happy enough that when it came time to close we were arguing over the discount; her wanting to give me the whole thing, me refusing to let her do that since she'd done such a good job. We compromised with me taking about half of the discount initially agreed on.
So... take away? The right agent can be awesome. Agents obtained via discounting services (and maybe the big firms?) seemed to be primarily looking to move volume... I'd avoid. However, you can likely use the existence of the discount services to negotiate rates down.
And don't be afraid to "fire" an agent, at least in my area you don't sign any agreement for exclusivity (or anything) so don't be guilted into continuing with someone who isn't serving your needs.
All that said, I do wish that the payment structure was different, because as you say, it does lend itself to just getting the transaction done, not getting you a good price or the right house. I've toyed with offering different commission structures and/or hourly fees in the future if I wind up needing to buy/sell again. I do think that alternative fee structures could do a lot to align the realtor's interests with yours. As an example, say you want to sell your house, aren't in a hurry to do it, and are wanting to get a good price for it. Assume $150k would be a reasonable price to accept if you were interested in a quick sale; then offer the agent 1% + 20% of the delta from $150k. So if it sells for $150k they get $1.5k, if it sells for $160k they get $3.5k (more than the "standard" 3%). If they pull off $170k you're both golden. Their goals are now aligned with yours. Of course this requires you and the agent to be in agreement on what the quick turn around price is. But... good luck getting something like that standardized.
And one last thing since I'm rambling on. I think the reason we don't see fee-only realtors is that the current system lets the fee be hidden and rolled into the mortgage so that it's not a separate payment. Majority of buyers wouldn't like thinking that every house they're viewing is costing them $50 or whatever... that'd start feeling really expensive really fast even if it's not costing them any more than the current way the perception of such is there. Hence... what we've got.