What got me about CFS2 was the 90 aircraft limit. If you think about it, I'm the one who has every single variation of every single aircraft I can get in each theatre of ops, so 90 entries - if you have two skins in the same aircraft cfg, that's two entries - is a real drag. That and not being able to use the turrets, as Clive says. (Which also makes holes in using Strike Fighters for WW2...)
The very best thing about CFS2 was the Mission Builder - dead easy to use, you're working directly on the gsl scenery so things are exactly where you put them, and you can fly the mission straight from the MB interface. Fantastic stuff! I did some ace missions, with loads of triggered events and things...