The UX disaster is not just about looking "clean" and "sleek". It is all about mobile. The choice between bland colored boxes, skeuomorphism and other styles is just looks, it doesn't change the fundamentals.

Here is the problem: smartphones have a small screens and are operated using fat fingers, so you need big buttons and you don't have much space, so you are very limited in the amount of stuff you can put on screen. It also means there is a lot of hidden stuff.

Now that having a mobile app, or a mobile optimized website is often a requirement, the desktop app usually follows the mobile conventions, which is not great, but better than doing it the other way. Having two entirely different apps to make the best use of the platform is possible, but it is expensive, and you want to maintain some level of consistency, so that users switching between desktop and mobile won't be lost. You probably want to maintain branding too.

To me, it is not that designers don't know how to do good UX like they did in the 90s/00s, it is that there are contradictory requirements and they have to make compromises.