The major difference between the two would be where the Processing for Plugins occur.
DAE will use the DSP Chips on the TDM Farm Cards.This eliminates much of the strain put on the CPU by power hungry plugins.You can NOT use MAS plugins along with the TDM Plugins.
Using Direct I/O with MAS (Motu Audio System) will now be totally Native Processing (uses the Mac CPU for ALL Processing. The DSP Chips on the TDM Hardware will NOT be used , but the I/O like the 888/24 ect…will be fully functional through Direct I/O)
You will then be able to use all of the MAS plugins (including 3rd Party MAS Plugins) with Digital Performer and the Digidesign I/O Hardware.
Which to use? The choice is yours!