I've completely gotten rid of the "ghosting" between lenses in ED. I tweaked the 3D settings in-game and have a pretty good 3D experience now. It's not as good as VR, but it's much cheaper, so it's not a fair comparison. I've also noticed that the 3D effect seems better with time; I think your brain learns to adapt to the anaglyph mode.
Since I wear regular glasses, I bought clip-on lenses (that flip up, like sun-shades). I bought 1 pair, saw the ghosting and bought 2 more pair. I've modded them, to use stacked lenses. The cyan lens shows more red ghosting, so I've stacked 3 cyan lenses (currently held in place by tape, but I plan to glue them around the edges with epoxy) and 2 red lenses. The image is dim, but looks pretty good. The ghosting is bad in ED because the worst case scenario for anaglyph mode is bright objects on a black background (eg. the stars and target marker). This doesn't appear nearly as bad in situations with less contrast. The image and video in the previous post look very good with my customized glasses.
You can also reduce the apparent ghosting by reducing the brightness of your monitor.
There's a bug in the ED anaglyph mode, which I have reported (weeks ago). The wrong color channels are used for the cyan blend, so red appears as yellow and green is missing. Even so, I prefer the ED version over the NVidia solution (described below). I mostly use the anaglyph mode when driving the SRV, which helps prevent the motion sickness that I often get in the SRV.
Another approach, if you have an NVidia graphics card is to use their anaglyph mode (activated in the driver). The colors look better, and there seems to be a little less ghosting, but nebula and the galaxy cloud don't appear to be at the right depth (the clouds appear to be inside your cockpit). There are tweaks available (using Reshade?? as mentioned in an older thread, but I never got it to work right).
The galaxy and system maps work very poorly in 3D mode, so I often turn 3D off (or just select a bookmarked destination). It would be great if FD implemented a key-binding to toggle 3D (or fixed the maps in 3D). I've written up a suggestion in the appropriate forum requesting this.