The effect of all those changes are numerous. For one, it is no longer possible to run the system without a graphical user interface unless you plan to invest a huge amount of work and to throw out most of your system support. If you want to get vendor support, this is not the way you will want to go.

You also can't implement complex network or authentication setups anymore. The number of possible combinations in the configuration has been significantly reduced by removing options which are not typically used for desktop systems. Also, since the APIs have a tendency to change very frequently, typically, only genuine supported Gnome or Ubuntu/Fedora software tends to work on the long run. If you try to use an alternative which has an user interface you prefer or has a feature you want, you will find very frequently that it is trying to call some DBus interface which is no longer implemented or has a different set of parameters.