It is a complete re-write of the old GUI with a different widget toolkit (Qt instead of wxWidgets). There are several reasons for such a re-write, among them:
The old code base would have to be re-written considerably in order to support things like changing the properties of more than one track at a time or for implementing multi-threading.
The cross-platform support in Qt is simply way better than in wxWidgets (e.g. there are several cases in wxWidgets in which the toolkit doesn't abstract away the platform differences and my application code has to work against that with several #ifdef clauses).
The Qt toolkit is much more complete.
The Qt toolkit has the better tools available.
The Qt toolkit is simply far more pleasurable to code against.
Back when I started writing the old GUI (around 2003), I was looking at the cross-platform toolkits available at the time. I actually wanted to use Qt back then already but unfortunately Qt was only GPL'ed for use on Linux at the time; in order to use it on Windows, you had to get a commercial license. Fortunately this has been solved a long time ago and Qt is now completely Free Source/Open Source for use everywhere.
What happened to mkvmerge GUI?
mkvmerge GUI has been deprecated in 8.0.0 and finally removed in 8.4.0. It hadn't been in active development for more than a year before that. It has been superseded by the actively maintained and much more powerful MKVToolNix GUI.
Please switch to MKVToolNix GUI and give it a chance if you're still using the old mkvmerge GUI.
Hint for new users
The new GUI uses context menus (those that open when right-clicking somewhere). Try that in places like the file/track list or the attachment list.
I've created a couple of short videos showcasing different features and how to use them. If you would like such a video for a feature for which no video exists yet, please drop me a line.