Asaki:
DJ's GOUT V1 and V2 are almost the same - the only difference is the V2 moves the (yellow) subtitles from inside the letterboxing (as it is in the V1) to inside the frame itself (V2). Also, the slow-motion scene in Empire (magic tree) required different settings for stabilization, which weren't applied to the V1, but were applied to the V2.
However, the V1/V2 used the same settings for everything else - which tended to scrub out too much grain and resulted in a loss of some fine detail. As a result, it appears to be cleaner, but when you compare it to the GOUT, you can really see how much detail has been lost. Edge enhancement is also an issue.
The V3 is an attempt to rectify these issues - stabilizing the image and cleaning it up without losing a lot of detail. All the samples I've seen from the V3 script look substantially better than the V1/V2.
It will also feature recreated theatrical (white!) subtitles, and all the available audio mixes for all three films.
ikjacc:
I doubt that DJ will be making an h.264 MKV version available. That's what I'll be doing for my own personal collection, but I doubt DJ will be doing it himself.
Also, even if he did, I'd prefer the alien subs to be burned-in the same way they will be on the DVD, as even SSA subs won't look right when viewed on my Seagate FreeAgent Theater+, and I'm really looking forward to having the proper, theatrical-accurate subtitles for the first time.
Kenobius Prime:
In the first few pages, AVCHD was indeed discussed. But the idea was dropped very quickly, for the same reason Frink said.