And I heard somewhere that Gnome is very popular in the US, but everywhere else KDE is slightly more favored (apart from all the small DEs and WMs).
Also, KDE (until very recently) wasn't helped by it's unusually hideous default theme and icon set.
For me I used to prefer Gnome because of the apps I was using. OpenOffice or Firefox seemed to be out of place in KDE. Plus I preferred a simpler environment, of course nowadays they've gone overboard.
Part of the reason is history (if we're talking about 15 years ago then Qt had a more restrictive license - and, sad to say, the gnome website still spreads FUD about this, or did the last time I looked). But mostly I think it's that big distros have Gnome as the default - probably because it's easier to support since it's much less configurable than KDE.
(And I don't think it's a clear case of one being "more mainstream"; rather, my impression is that Americans tend to use Gnome/GTK and Europeans tend to use KDE/Qt)
That's the main thing I don't like about it. Also I don't get the depressive trend of washing out colors and turning the style into monochrome. What's wrong with colored icons?
I hope there will be a way to chose other styles and KDE will maintain the reputation of being very UI configurable.
So no, customization never went away. Breeze is just replacing Oxygen, but the ability to change it doesn't go away.
The state of WMs on Linux is really, really more complicated than it needs to be.
Choice is always going to be a prominent force in Linux. There will always be folks who are going to write new toolkits and apps and there they will find users who would want to promote it. That is just the nature of Open source.
That being said I think no one really likes to use GTK+ app if they are targeting multiple desktop environment and operating system. Ubuntu's Unity 8 and KDE both are using Qt and Qt is already available on all possible platforms including Android.
IMO, its more of an inconvenience than a big deal breaker.
Should an application (let's say, Amarok) require chunks of KDE to install on your nice GNOME desktop, your package manager will install those required packages along with the application, so that when it starts up, there are no missing libraries or errors. And those libraries will be loaded (in the case of Qt4, 50MB of libs) into memory for as long as the application is running.
Now, should you be running a headless install without all the appropriate lipstick packages already installed (some of us like running X apps over SSH sessions), you may see some really ugly naked widgets. Qt and GTK+ without any theming engine installed will not win any beauty pagents, but you'll be able to use the application, even without icons. And, should you wish to place some lipstick back on that pig, you just need to install a package or two to pretty everything back up.
TL;DR - Stuff should work fine between DE's, if it doesn't, then your distro is broken or frankenstein'd.