The biggest problem I had with switching was the TDC.
It just seemed so much straight forward in the SH3 (with mods). I found the physical arrangement of the TDC and the data entry locations to be awkward and slow compared to SH3.
It was a pretty humbling experience to go from SH3 where I was able to do manual targeting very quickly, even with multiple targets; and then do to SH4 where I could not hit a bull in the butt with a base fiddle. I am getting better at SH4 but not as good as I am with SH3.
Both games are fun though