Yeeahhh, I have ran into issues definitely. When I was trying to make a 32 bit KDE I ended up using a 12.04.3 and running a dist to get around problems I was having with 13.04 and .10. It did work, I can't remember the specifics though, the GUI was limited I think, so it was either drop Remastersys or go backwards. There were other issues, like Firefox only wanting to use Nautilus and I ended up dropping. In truth I am more trying to unravel 13.04 with latest updates at the moment, but I will run a Remastersys any minute now.
I am pretty positive remastersys is not how I want to build but I am limited in knowledge and ability. I like the mechanics of Puppy Remaster a little better as there is more control in file management, with remastersys you sort of have to see it as setting up an empty session for the live/new user. This can get complicated since it is a little better to stay off the system with user mannerisms, internet, etc. Last thing you want to do is release a system with all your personal information and hardware settings attached.
With Cinnamon, there were issues with Multi-De more so than running straight Cinnamon, so say if you are running a straight up say, Nadia Cinnamon, you really shouldn't have that many issues, depending on what you are trying to do. Oddly though when I hear of a really sturdy and steady Mint system it is usually in reference to Mint XFCE, not Mate or Cinnamon, and since I do not believe them and have no intentions of finding out I will just have to take their word for it. If Cinnamon can run on its own that's great, but that doesn't really mean that there won't be issues when installing Gnome 3, or that a version of another DE won't cause problems, like with Unity and Gnome. Last Multi DE system I ran dist on actually removed Unity and replaced it with the new Gnome Classic. The new Gnome Classic, btw, is very much like Cinnamon, and now Fallback is very distinct from that style. If I were to bet, I would bet that the latest Gnome 3 will cause issues with Mate and Cinnamon. You can still take LTS 12.04 and make multi DE happen because by LTS nature you should default out of the cutting edge because I mean, that's not the point of the LTS. If you are in the habit of update/upgrade on top of Multi-DE with the latest and greatest you are going to have issues. Lot of them. You kind of have to choose your direction. So if say, I wanted to use Cinnamon with another DE, I would probably install Mint. Since 13.10 just released I would twiddle my thumbs for a minute and then grab 16 and go from there. Thing is, you need to know how the DE runs on it's own before you can really determine what is causing any issues.
If I really wanted to emulate Windows though I would still use KDE. Least then I can still pull out the bag O' Eye Candy tricks whenever I wanted to. Gnome 3 is just horrible though. Intuition be damned we are GNOME.
