When I got my Ref6, I compared it to the new Foundation LS28, as my shop didn't have a Ref5SE on hand. I was actually intending to get the LS28 or find a used Ref5SE, but my dealer, who I've worked with quite a bit, had a Ref6 that a good customer had traded in to upgrade to D'Agostino. The price was (relatively) not too much over the price of the LS28, and there was only about 400 hours on the Ref6. My research at the time indicated that people thought the new LS28 was pretty close in sound quality to the Ref5SE.
The LS28 was good, but the Ref6 was immediately noticeable as being better. Everything was more transparent, and there was a definite improvement in the quality of the bass. When I notice a difference so easily after the several minutes it takes to switch out cables, I'm confident that it's not a small improvement.
I'm going to offer another observation, though. When the new B&W 800 D3 series came out, I went in to upgrade from my 804 D2's to the new 803 D3. I ended up selecting the also new Wilson Sabrina instead, and have been very happy with them. Last summer, though, my dealer offered me almost what I paid for the Sabrina's to upgrade to the new Yvette. I spent a couple of hours listening to them side by side, through the same gear I'm driving my Sabrinas with at home, and there was no question that the Yvette is a significant step up from the Sabrina. BUT - once taxes were taken in to account, it was still going to be around $13,000 for the upgrade.
I spent a few days thinking about it, and realized that I was still very happy with the Sabrina's, and if I weren't listening to them so close together I'd be hard pressed to say how big of a difference there really was.
The upshot? I probably would have felt the same if I got the LS28 instead of the Ref6, especially if I could only get the Ref6 at the new price. My recommendation is go with a used Ref5SE, get used to its sound in your system, and figure out if you really want the Ref6 when you come across a used one that's more affordable for you.