Unity 5.3 arrived last night, with some nice new improvements. Upgrading was painless.
They now have multi-scene editing, which looks interesting.
Currently we have multiple levels in each scene, split between me and Rob doing the design. We do this because it's very useful to have different levels easily accessible, so we can check things, or copy and paste parts from other levels.
On my current task list is a tool to split the scenes up in to multiple scenes, one per level, to make loading quicker. I deliberately avoided getting on with this task because I knew the new Unity version was coming out soon.
It looks like it was a good decision. I think we can now have one level per scene, and still have all the other scenes on-hand as reference. I'll be trying it out in the next week or so, but fingers crossed, this could be a big improvement.