2) He changed the background color lighter to show more contrast on the blur, even though bg colors are customizable in twitter, thus creating an unfair comparison.
3) Top black bar items not aligning with the grid may have been intentional. It's not part of the layout but intended to be a separate object that is part of the view port. I'm sure it was intended to seem like the bar was an extension of the browser, not part of the web site. In this way, it does not distract from reading.
4) His contrast with background colors on the "tweet box" area, the feed, and the right side was done poorly, completely breaking the concept of main vs sub content on left and right. The original background colors are much better in clearly segregating left from right, and devaluing content on the right.
Designers forget (esp those with print backgrounds), UX is not simply about making things look pretty, but also being able to trigger an emotional response and create a connection with the end user.
Ironically, Doug Bowman's latest post on StopDesign talks about the Uncanny Valley. This theory applies here too. Rodrigo's design looks way too much like a static blog, and makes me feel uncomfortable.
Although aesthetically pleasing at first sight, this guy still has a lot to learn from Doug Bowman.
His design honestly looks like a Wordpress Blog theme, not Twitter.
I know UX people like to claim they are responsible for the user experience but this is really not true unless they are able to actually visually design the site too as the visual part is the primary emotional trigger.
This is why all UX people should be able to design.
The problem with his twitter redesign isn't about the emotional response but simply about the information design. It's badly done and reduces the ability to scan the page.
But other than that I agree completely.
That said I agree with the rest of your critique...