The 40 inch.. hands down!!
The 40 inch is a proper RO designed for heavy use. It will give much better TDS reduction than a merlin. more output, and far..far less waste water. Some people will run a 40 inch system at only 20% waste but in a hard water area you are better at a 50/50 split.
The Merlin will chuck out at least 3 parts waste to one part permeate (processed water) but usually more like 5 parts waste to 1 part permeate. I am in a hard water area and the guys I know who have a Merlin get at best 90% TDS reduction so they eat resin. Especially those who use quite a bit of water every day.
The 40 inch will have 2 prefilters whereas the Merlin just has 1 x carbon filter before the membranes. I suppose if you are in a soft water area and dont care about waste then the Merlin would be O.K. but if you have a choice go for the 40 inch system.
Its a pretty simple equation in that the less TDS reduction you get from your RO the more resin you will use so whichever one is better at TDS reduction has to be better providing it gives you enough water for your needs and the 40 inch will give a much better performance on both counts.
OOPS

For got this: Membrane replacement is pretty much the same cost. For the Merlin you need the set of 2 at about £85 each and a good, E.G an Osmonics Desal low energy 40 inch one will be around £185.00 but you will probably replace the 40 inch one at much greater intervals than the merlin ones.