I've seen this article before, and it paints a really ominous picture of the road that the auto industry is careening down at breakneck speed. The worst part of it is that they haven't given an indication of reversing course away from direct injected 4 cylinder engines in any significant way, in spite of all the problems being reported. The Atkinson MPI is one, but I'm not aware of any others. I'm becoming resigned to the unhappy prospect of getting stuck with an engine I really don't want in our next vehicle. Very unfortunate to say the least.
The article is pretty good overall, but...
He misunderstands why a carburetor needs an accelerator pump, yet MPI and GDI don't need the equivalent.
He also doesn't understand the principles and advantage of stratified charge.
Honda was successful with it starting back in 1975.
Having a lean condition around the perimeter of the combustion chamber actually reduces the amount of fuel that collects on the cylinder walls etc.
Having a rich condition at the spark plug starts combustion more quickly and robustly.