Please don't do what happens when you upgrade NMM - which is to force users to update each mod again. What need is there for that sort of nonsense unless your adding something to each mod? Which you don't... Just don't get lazy again and create the tools to read through your own data you built with your own app.
Sure there seemed to be an auto-update, but don't do this again unless you have a lot of error trapping, handling and timeout loops that can prevent what happened to me... a lockup on upgrading mods (waited 1 hour and it didn't update anything).. and the result the upgrade crashed all mods (reloaded 255+ mods again) because of how NMM upgrades itself. I still had the plugin.txt to work from, so that was okay to play the game, but NMM was blown apart. What was horrible was that it created the problem, and had not one ability to fix itself. Oh sure, I did the purge, and all that did was wipe out all the mods I was told by the authors to manually plug into the DATA folder.
As for the Nexus website. Nice more flat design and web-responsive. The upper area where the banner ad content has a huge amount of wasted space if the advertiser puts in a lower resolution image. So you end up with a small box of ad with 2 inches of wasted space and makes the overall site look cheap and banner ad focused like GEOCITIES of old... but the search is much improved and industry standard at the top of the page. Heavy use of tabs.
Being a gamer site, I'd have more liked to see user-preferences for users to select their skin/theme of their choice.
Button color selection is not well-done. Orange? That's not a recommended primary selector color when you overuse it for all hyperlinked material. Again, maybe theme selectors would have been nice, but better than the original site.