One thing Blizzard likes to slip in every few patches is a new UI function that "replaces" a popular add-on or set off addons. They've done it with Scrolling Combat Text, Threat Meters, and most recently, with Equipment Managers.
The New Equipment Manager is nice, but it's also pretty basic. You choose to save a set, choose a name and icon for the set, and there you go. You can drag the new icon onto your toolbar for quick changes, at least, but there's not much else. You can't synchronize it with a talent change. You can't set events to automatically change sets. Because of this, or even because of straight up familiarity and the issue of remaking all your sets in the new system, I'm sure a lot of people will stick to addons like ClosetGnome and Itemrack (if it ever updates).