The following comments are just my opinions, and other people may have differing opinions.
If you intend to connect a keyboard or controller to another MIDI device, then it would be best to get a keyboard/controller that has MIDI ports, because you'll be able to directly connect the two devices together using just MIDI cables (assuming the other device also has MIDI ports). In contrast, a keyboard/controller that has a USB-MIDI port can't be directly connected to another MIDI device, because it must be connected to a USB host (typically a computer). Most USB-MIDI adapter cables can't act as USB hosts, although there are some USB-MIDI interfaces that can, such as from Kenton and iConnectivity. So it's certainly possible to connect a keyboard/controller that has a USB-MIDI port to another device that has MIDI ports, but it requires more than just a connecting cable:
Simplest: Device A (MIDI ports) -- MIDI cables -- Device B (MIDI ports)
Not as simple: Device A (USB-MIDI port) -- USB cable -- USB host device -- MIDI cables -- Device B (MIDI ports)
Won't work: Device A (USB-MIDI port) -- USB-MIDI adapter cable -- Device B (MIDI ports)
On the other hand, if you intend to connect the keyboard/controller to a computer to use it with MIDI software (a DAW, notation program, soft synths, or other virtual instruments), then it would be best to get a keyboard/controller that has a USB-MIDI port, because you'll be able to directly connect it to the computer using just a USB cable. Most computers don't have MIDI ports. Of course, you can connect a keyboard/controller that has MIDI ports to a computer using a USB-MIDI adapter cable, but inexpensive USB-MIDI adapter cables can be problematic (read: a POS). Also, most households are more likely to have a spare USB cable lying around than a spare USB-MIDI adapter cable. So if you want to connect a keyboard/controller that has MIDI ports to a computer, you'll need to buy a decent USB-MIDI adapter cable (and hope it works with your MIDI device), or buy an audio interface that includes MIDI ports (which you've apparently already got), or buy an internal sound card that has MIDI ports for your computer:
Simplest/least expensive: Device A (USB-MIDI port) -- USB cable -- Computer
Simple but slightly more expensive and prone to faults: Device A (MIDI ports) -- USB-MIDI adapter cable -- Computer
Simple but even more expensive: Device A (MIDI ports) -- MIDI cables -- USB audio/MIDI interface -- USB cable -- Computer
Simple but most expensive: Device A (MIDI ports) -- MIDI cables -- Computer with internal sound card with MIDI ports
So the bottom line is that you can use either a keyboard/controller that has MIDI ports, or one that has a USB-MIDI port, although which type is best can depend on what sort of devices you intend to connect it to, as well as how simple and inexpensive you want the process of connecting the devices together to be.
Of course, the ideal choice would be a keyboard/controller that has both MIDI ports and a USB-MIDI port, to have the best of both worlds.
But to get back to your specific question, there's no real advantage to getting a keyboard/controller with MIDI ports and connecting it to your Babyface Pro versus getting one with a USB-MIDI port and connecting it directly to your computer.
EDIT: That's assuming you're only ever going to be using it with a computer. If you want to leave open the possibility of connecting it to another MIDI device at some point in the future without needing to go through a computer or buy a special USB host MIDI interface, then it would be more advantageous to get one with MIDI ports.