Okay, so I've read through the PDF a few times and let it percolate a bit.
One honest question before the actual feedback: Why massive rule shift? Please note, I'm not one of these "OMG new rules suck!" types, I'm honestly curious what the underlying reasons for massively changing so many sections of the game were because the most common complaint I heard, from both my players, and others on the DH/RT/OW boards was that each system was subtly incompatible with the others in very annoying ways. One generally does not solve a complaint like that with making a new revision that is even more incompatible with the rest.
I could see someone being brought on board and deciding to "leave their mark", in effect making rules for rules sake. If that's the case, I would caution you that it will likely not end well. I can't tell you how many times I've seen senior folks who wanted to "leave their mark" come in when I was in the military, change a bunch of stuff that worked, and then couldn't figure out why their changes caused mass chaos and unhappiness. Change for change's sake is never a good thing.
That said, after thinking about various changes and points, I've come to a few conclusions, some positive and some not.
1. The new rules as a whole, do not really fit the game system as it was, nor do they even begin to align a 2nd Ed. with any of the other game systems. I don't mean this as a slight against the designers, though I realize it is terribly difficult to put so much time and effort into building what you believe to be a better system and then to hear negative criticism... well, nobody likes to hear their baby is ugly.
2. Some concepts behind individual rule changes are quite valid, if not better inspired than the original versions. Character creation is a good example of this, despite not being terribly fleshed out and having a few 'change for change's sake' aspects.
3. Some concepts behind group rule changes (ie. systems) don't make a lot of sense from a design perspective unless they are change for change's sake or that the devs are trying to address a meta-problem I haven't noticed yet. The complete rework of the combat system to an AP based system is a decent example of this. Not sure what issue they sought to address with this, and if the added complexity is worth it.
4. Why alignment was important and what this means overall -- As mentioned above, it was the most common complaint, and it was that way for a reason: each successive game system tweaked different aspects of the game, introduced rules to deal with systems unique to themselves, but in doing so, little work was evidently done to try to maintain compatibility, both in terms of raw rules, errata, and the like.
Each system was a project in and of itself, and you could find the same item having 2 or more different stats, forcing the GM to pick which stat he used if he, like many GMs, was running a cross-game campaign. This is pretty important when you consider some games like DW were tuned for high damage output and nasty critters, while others weren't... quaint kludges not quite compatible with fluff/canon to justify the differences between Space Marine items and the rest were barely acceptable.
This subtle incompatibility got worse as time went on... RT characters scaled differently than DH characters, DW characters were generally walking Baneblades compared to other game characters (I mean, they're Space Marines, so that's kind of the point...), OW types dropped the leveling scheme altogether until HoE came out... all in all, the various systems only vaguely resembled each other past a certain point.
Considering games like RT and DW were far more niche than OW and DH, it isn't reasonable to assume that they'll get a 2nd Ed. any time soon, if ever so this 2nd Ed as it stands makes the incompatibility issue even more so, pushing far more work onto GMs. That's sloppy.
(Warning: some may see this as a shameless plug. It's not intended as such.)
IMO, what the Franchise needed more than ever was a clean rebuild from the ground up that harmonizes all branches in a non-suck manner. That said, from a business perspective, I don't know if FFG would go for that... or if they even could, legally, seeing as we don't know what their contractual obligations and limitations when it comes to the various IP are.
I would like to note that a unified ruleset would not necessarily have to be be just "DH/RT/OW/etc using OW rules" ... as I said earlier, there are some very good ideas found in the 2nd Ed. and I highly doubt any reasonable person would complain about those good ideas being implemented, were they done so smoothly and completely.
Regardless, I doubt anyone really wants to hear about my project, and most seeing even this brief mention would probably see it as shameless self-promotion or arrogant competition with the 2nd Ed devs. Honestly, I think it would be interesting to pick their brains directly to see why certain changes were made and see what they made of the alternative paths I chose to go down, but it's a bit late for that, seeing as FFG has invested as much time and money in 2nd Ed as it has so far.