If the "skins" were just preferential type changes, that would be one thing. But many of the fixes within HN Enhancement Suite are basic UI fixes.
Making links in profiles and text posts clickable. That's like the most basic thing you can do for your users.
Adding the ability to collapse a massive comment thread without having to scroll to the top. Also, indent guides (especially needed for the massive threads around here). Shit, HN didn't even have collapsible comments for the longest time.
Being able to comment inline and not having to navigate to a separate page where you lose context of the surrounding discussion.
Highlighting new comments since you last viewed a thread.
These are all basic things that HES addresses, there are many more I can point out. I'm not trying to insult the admins, I think they do an amazing job of running the site, but let's not pretend HN is some pinnacle of UX design. We are all just very used to it.