They had correlation issues between the the CFD and the real track going back to 2011 / 2012, even though at the time their car was doing okay they couldnt understand why as it was outperforming their data.
Evidence of the "theoretical" cars goes back to their trademark stiff chassis that seemed to spend more time on 3 wheels than 4. This was because their aero was more pitch sensitive than any of their competition meaning their car had a much narrower performance window and was also much more difficult to set up.
IIRC their first car of this more exploitable downforce was the 2014 which didnt go very well so as the season went on you could see the car getting stiffer and stiffer .. back to old ways.
Fundamentally the team have 3/4 brand new cars in a row all based around different concepts. This years is probably the first one that is more of an evolution and you can see that in the slightly improved results. Every year we get press releases from Mclaren blaming their lack of performance on one thing or another and promising WDC "next" season. I cant see that there is much difference between the Renault PU and the Honda PU but RBR are able to put the Renault on pole at Monaco. While Mclaren remain 1.7s off the pace.
We saw that Mercedes spent 3 years preparing for the change in regs and it has taken the other teams 3 years to close the gap. I would have expected Mclaren Honda to be taking advantage of this lesson and trying to make strides up the grid for next year rather than saying they are focusing 50% on it when we are halfway through 2016!