Sorry I've been MIA.
So, the ONE.3 has a completely different layout and the sound quality is the same as the iMake ONE.3. The iMake ONE.3 has a different but no better pre-amp section, and the same amplifier board.
Folks who have had them both (TWO.x and ONE.3) notice the higher gain on the ONE.3 immediately. After all, it has a 2.5x active pre-amp inside so it gives a lot more umph with low-power sources.
It's also true that the layout is improved so we're getting slightly cleaner Tripath sound and lower EMI (FM radio interfrerence).
However, the difference from TWO.2 -> ONE.3 is slight if noticeable. The TWO was an extremely nice unit with pure copper posts and audience caps. I'd take a TWO.2 with batteries over a stock ONE.3 any day. However, the original TWO did not allow batteries and for those customers, the ONE.3 would be a nice step up.