No difference
I now play slots regularly, but usually when some kind of bonus or loss insurance promotion is on, or for a tournament. I rarely play the non-bonus slots though, except for 5-Reel Drive, Carnaval and What A Hoot, along with the 800/1600 jackpot 2 coin 3 reel slots to meet a WR with low variance.
On small stakes I use autoplay, although on larger stakes I use either manual play or the 5 and 10 spin buttons.
I have found that manual play can be just as unforgiving as autoplay when it comes to getting the 3 scatters, and autoplay can give the scatters freely too.
One thing I have noticed though is that the scatters either come within the first 2 or 3 dozen spins on autoplay, or not at all for near on 300 spins. I have gone 700+ spins on Thunderstruck with no 3 scatters, and much of this was on manual play on a medium stake in the range.
On a small stake of 0.45 and on autoplay I hit wild hammers in the bonus round. I also hit 5 scatters on Spring Break during a bonus round that was triggered during autoplay, but which I had set to stop for me to enjoy the free spins myself.
I don't think it makes any difference, and according to the rules of random games it should not. Any long term evidence that autoplay wins less or more than manual play, or that stake and coins played makes a difference, would be rather damaging for the credibility of Microgaming. If anyone has such evidence, or thinks they have, it should be posted so that we can all form our own opinions.