I agree with you completely! I’ve been decorating cookies for years, and I still struggle with icing consistency. It’s still a mess and a pain to make all of the colors. I don’t think you’re missing something; that’s just kind of the nature of the beast.
Like Manu, I start with stiff-consistency, uncolored icing and just portion off small amounts to color and thin. I mix each color in a small bowl, thinning with a spray bottle of water, and then I store the colored icing in a tube of plastic wrap. (See this post by Sweet Sugarbelle for a better description.) With the plastic wrap method there is no crusting. I keep these pods of colored icing in a big ziploc bag in my fridge for weeks. They will start to separate after a time, but then I just cut off the top, squeeze the icing into a bowl, and stir it again before giving it a fresh plastic wrap tube. (Or if I’m feeling really lazy, I’ll just massage the icing within its original plastic wrap.)
It seems like everyone does things a little differently, but this is the method that works best for me.