The UI is clean and modern, what do you mean?
By clean and modern do you mean ugly and old web-2.0 style?
By simple, i mean something like jenkins.
By modern, i mean something like github / outlook.com online app.
More substantiated critique:
+ Background is too distracting / there is no clear separation between the background and content
+ Buttons don't fit well with ANYTHING on the repo page.
+ Ugly borders around things / the line below logo
+ The login thingy (WHY is there a line below it?) isn't clearly separated from the background / other content
+ Search options [Title/...] on all pages would look better if replaced with Advanced search page
+ CSS animations look weird, they should be a bit faster, imo.
+ Orange and Blue don't fit well together.
+ If you click on plugin description weird blue outline appears around it in Chrome.
I would love to see some changes though. For example the background isn't really to my liking, and I prefer the plugins to be shown as a list with the first line of the description instead of a grid without any information except the name, creator and version.
Combining "Jenkins" and "Simple" in a single sentence gives me goosebumps

That's the strongest oxymoron I've ever seen

Well, i meant simple as in not many fancy Windows 8-like things.

Well, I changed the header style a bit, do you like it?
It looks better, also: the old background would be fine as long as it's visibly separated from the plugin list - that way, you don't have to look closer to know what is the thing you are looking for.
Ps. I think it'd be better to provide an old-fashioned list-like plugin repo, or a first page with those big buttons (featured plugins) and a category list on the side that when clicked shows you a normal list.
Why don't you want to make the plugin repo opensource ?
> It's because I don't think we want thousands of repos popping up from nothingness. We want on central place for plugins, don't we?
We can just tell git to ignore the data directory.
, Could you add a mailing service for when someone commented on your plugin?