This is actually probably good news. Was it 10.4 that shipped with a broken version of XQuartz and we had to go download the new version anyway? I know it was a rather annoying issue back when I used OS X more frequently.
It could be a bit smoother, though. When you launch Java you just have to click twice (once to install, a second time to accept the terms), wait a few seconds until it downloads and installs, and you are done. Everyone can do that, it’s smooth and it’s nearly impossible to go wrong.
When you start X11 you get a similar dialog, but it currently sends you to a website where you have to download stuff. That’s not the same.
It’s no big deal, really, but it could be smoother.
In the cases of Flash and Java, possibly also trying to disclaim responsibility. We often see statistics about security holes in MacOS vs Windows; those made based on Snow Leopard or earlier tend to include Flash and Java security holes for MacOS but not Windows, because, while most OEM Windows devices do ship Flash and a JVM, Microsoft does not.
All this changes is that the first time you run an application that uses X11 a dialog box pops up directing you to the XQuartz project page.