First of all, don't panic. Nothing that has been changed — including especially the striping of the Chatterbox — is set in stone. Things are being worked out. There are a lot of organization and compatibility issues to address on a complex site like this, so it will take some time.
Caution: Contents may have been coded under pressure.
Discussions are ongoing in the chatterbox as the volunteers tweak things. They do want input on how you like or don't like changes. Be pleasant when providing your input. We're all on the same team, here.
Meanwhile, if you don't like the way some feature is colored in your favorite theme, you don't have to give up the theme entirely. You can override the undesirable setting in the "On-Site CSS Markup" box of your Display Settings. In particular, you can negate CB striping with this snippet of CSS (courtesy of ambrus):
Stay tuned.tbody.nodelet td.highlight { background-color: transparent }
Caution: Contents may have been coded under pressure.
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