Honestly, the more I look at this comparison picture, the more it looks like the new ship isn't as out of proportion as it appears.
If you look at the base of the support pylon at the top of the secondary hull, the distance to the saucer appears to be about the same. And the overall diameter of the two secondary hulls look to be about the same as well.
Where I think the new picture is throwing us off is a combination of four things:
1. The underside curve of the secondary hull is a lot further forward forcing the look that the deflector dish has been moved in relation to the saucer.
2. The oversize support pylon (and structurally more realistic) swooping further back is also adding to the illusion of a smaller secondary hull. If you look at and compare the TOS secondary hull to the Refit, you'll notice that the TOS has a smaller overall O.D. (by about two decks).
3. The picture seems to also be a forced perspective, causing the parts of the ship to distort. Look as to how huge the saucer appears appears as it get closer to the "camera".
4. Over the years, we've seen the different incarnations of the Enterprise (and other starships), the one subtle thing that was happening, was that the designers kept moving the deflector dish back. Now that the new team is trying to somewhat keep with the original intent, a lot of fans are having a knee-jerk reaction.
I think the biggest mistake was just their choice in the initial picture released.
I recall when I first saw the Enterprise D, I had a similar "shock" reaction. I thought it looked like "melted art-deco". Though over time, I grew to appericate and love the design.