Generally I don't have issues updating the look of the site and adding/tweaking features. The changes over the years have definitely improved things.
The fixed Slashdot banner at the top of the page is a major annoyance.
The reason I don't like it is the banner takes up too much space and now 1/3 of my browser estate is lost to view content.
I've seen other sites do this and generally avoid them.
Another issue(only one issue per comment? fuck you sue me) is leave the comment & moderation system as it is. This is a fundamental part of Slashdot and changing this means this site ceases to be Slashdot.
One of the major reasons I visit this site is because of the community and comments make the stories on this site interesting to read, funny and dare I say insightful.
The community is what makes Slashdot - send them away and the site dies. If you are trying to expand your audience you are going to lose to other competitors.
Where's Cowboy Neal when you need him? I miss my hot grits.
I also DO NOT welcome our corporate overlords.