One big question mark in all this is whether the mecha development setting info from The Origin and MSD is supposed to apply to the overall Universal Century history, or whether it's valid only in the context of The Origin. Technically, most of this has never been addressed in a "filmed work," so none of the previous material from third-party books and suchlike was ever official in the first place. I don't expect we'll get clear guidance on this from Sunrise any time soon, so in the meantime, it seems like a matter for idle fan speculation.

Anyway, before we get into the increasingly tangled history of the Dom family, let's consider the series of prototype mobile suits and mobile workers leading up to the Zaku...
http://www.ultimatemark.com/gundam/images/msd.jpg
The above is a lineup of the Mobile Worker Model 01 Late Type and Model 01 Final Type, the MS-04 from the comic, the YMS-03 Waff from the anime, and the standard MS-05 Zaku I. I did my best to get them all in proper scale, though I had to guess at the MS-04.
The thing that occurs to me is that the MS-04 really seems out of sequence. With its boxy legs and pelvis, proliferation of cables, and rounded chest armor, it looks more like a missing link between the MW-01 and the Waff. If it actually goes in between the Waff and the Zaku, then we have a situation where major design features flip back and forth between every version. Perhaps this will be addressed with a design makeover for the next episode of the anime, but so far the anime designs have stuck very closely to the comic, so we can't rule out the possibility that they'll basically stick with the comic version.
Personally, although I can take or leave the MW-01, I do like the Final Type (fingers crossed for a model kit!) and the Waff seems like a clever solution to the problem of designing something even simpler than the Zaku I. The Waff's round shoulders, two-part skirt armor, and bell-shaped legs even hint at a common ancestor to the Zaku, Dom, and Gyan; it's an ingenious bit of design.
The Waff's leg design also hints at the possibility that Zeon has now switched to a frame-based construction. Older sources claimed that Zeon mobile suits used a shell-like monocoque construction, where the armor holds the body together, while the Federation used a frame-based semi-monocoque method. But the MS Museum catalog claimed it was the other way around, and as we discussed in a recent thread, the anime seems to confirm that Zeon mobile suits are actually built on an internal frame that can function without armor. Page three of that thread includes a bunch of screenshots of Gelgoog and Kaempfer internal frames, and if we needed any further confirmation, we just saw a fully functional armor-less Zaku frame in Gundam Thunderbolt.
Once again, it's interesting to compare this with the earlier printed sources. As I noted in this Origin timeline thread, the MW-01 Final Type seems to roll out at roughly the same time that Gundam Century gives for the rollout of the MS-03, namely February of U.C. 0074. Gundam Century's description of the MS-03 says that "Zeonic attempted to dramatically reduce the weight of the third prototype unit, which was then under construction. The cockpit escape system was removed, and the body structure was changed to a frameless monocoque type." I might suggest that it was actually the other way around, and that the YMS-03 switched away from monocoque to frame construction.
Anyway, in episode 3 of the anime, Dr. Minovsky promises to complete the YMS-03 by the end of that year (U.C. 0074). In the comic, the next stage of mobile suit development we see is flight testing of the MS-04 in June of U.C. 0077. So let's see what the anime version shows us about the next few years of development history...
-- Mark