It's tricky, I thought about getting the little trays but you're totally right I think it defeats the entire purpose of the skirmish type movement capabilities the new format requires for good tactics. I saw some cool third party alternatives that have more shapes and stuff but it comes down to I guess using some trays for the bulk and then keeping some loose for the edges, if that makes sense.
It sucks because I do really love loads of skeletons! But at the same time, as I am still learning all the units and stuff, I am thinking about fielding forces of units like Vargheists and Zombie Dragon and stuff like that for a while, for ease of learning and speed of play, like I'm aiming to just play lots of games to get more varied opponents and learn the rules for races.
I really was cautious at first.... but now I seriously love all the new detailed models, back when I collected Warhammer a lot of stuff was still metal. I've gone a bit mental and already have a pretty big army to paint!