I've a 1999 Makarov and 2011 version

I'm sure you have read the reviews or perhaps seen the spot the differences videos on YouTube (if not have peek).

The obvious cosmetic differences are the now cast slide, it is lighter and thinner on the 2011 vs the heavy machined version on the 1999, in addition the 2011 has a cut away by the firing pin, the sight line is narrower (4 dots vs 5) and the rear sight thinner as well. As the slide is thinner this accounts for the gap which people mention and you can look down and see through the ejection port.

2011 has a cut away in the hammer, the 1999 as well as solid has a hint of red to the metal which is what the real steel have.

The sear spring looks slightly thicker but not much on the 1999. 1999 has the bigger authentic grip screw.

I would say the lower frame is identical though.

One thing I did find though was that when I put my upgraded magazine in the 1999 I'm not getting as much power as in the 2011 model (highs of 427 FPS vs 492). I have put an upgraded breech seal in the 1999 so it should be the same.
I also found that gamo lead are as accurate in both, yet if I use copper coated steel BB's the 1999 shots about 5" higher (not poa)

Here is a photo comparing slides, spring, hammers, screws
http://instagr.am/p/UYZ6cqEQmA/

This is a side by side look and you can see the 1999 has the beard slide.

http://instagr.am/p/UOVoUSkQql/

I prefer the 1999 for the look at weight of the slide, but was and am still happy with the 2011 and all in all think these are great little pistols.