Obviously one of the biggest differences is price. The R4 retails for $1600, the 744 for around $3900.
The R4 has phantom power available on all 4 inputs, the 744 does not.
The 744 can record to CF cards, either instead of, or at the same time as, the HDD. The R4 only records to the harddrive, the CF slot is only there for transferring to/from the HDD...no recording capabilities.
The 744 has 2 digi inputs, one for each group of 2 channels, the R4 only has 1 digi in.
Similarly, the 744 has 2 digi outputs for each group of 2 channels, while the R4 only has one.
The 744 has timecode synch and wordclock output, the R4 does not.
Most importantly though, the 744 likely sounds a lot better as an all in one solution. While the R4's pre/AD are definitely an improvement over the UA5, and pretty damn good, the 744 really is in a class by itself...one of the main reasons for the more than double price tag.