Thess are the limitations [of the 1.8] I know so far when compared with the F/1.4 version.
1. Build quality. The lens is not well built. But it doesn't mean it will fall apart anytime soon as long as you take good care of it.
2. Less shutter blades. The F/1.4 version has more shutter blades so it create a better out of focus background type shots than the F/1.8 version. (8 blades vs 5 blades)
3. Slower AF speed. The F/1.4 version is a USM lens so the AF speed is faster and quieter. And it has a Full Time Manual Override AF mode. (But I do not mean the 50mm AF is slow, it is faster than some lens I saw)
4. Plastic mount vs metal mount. It may not make too much difference, but I just like metal mount lens.
5. Depth of Field (DoF) scale. The F/1.4 has a DoF scale.
6. Manual focus ring on F/1.8 MKII is a tiny little ring which position in the front of the lens. Sometimes it is a little harder to use.
7. F/1.4, of course it has a wider max aperture than the F/1.8. And because of the wider max aperture, it also help in AF.
8. According to the MTF data from photozone, optically, they are about the same from F/4 to F/8. But the F/1.4 version is sharper from F/1.8 to F/2.8
9. Of course, because of the way the F/1.8 version is made, it weight less. But then again, the F/1.4 is not a heavy lens.