What would you choose and why?
I've used both as well.
Both produce pretty well though the 4040 had the edge.
As already stated, Merlin takes up a bit less room.
TDS from merlin is generally higher as they're not the cleanest of ROs - especially as the membranes start to age.
Another issue is whether water is metered or not. Merlin produces a lot more waste than a 4040 - though this can vary depending on the setup.
So I suppose it depends what you want really.
I currently run a merlin.
I only released the 4040 as it went with other stuff I was selling at the time.
In my current setup I'm tight for room, need to keep the waste down as it runs into a ditch, but high production and low TDS are not the main issues - so a tough call really. As with most questions like this, there is no definitive answer as it depends on the individual circumstances.