Yes, it sucks you paid all that $$$ several years ago for the MFC and now it is out-of-date. But, it is far from useless with the AxeFX3. Some of the integrated things that worked with your AxeFX2 might not be integrated on the 3, though. Don't let this stop you from getting the 3, it's an awesomely powerful unit with fantastic sound capabilities. I used a 20-year-old fossil Roland FC200 with mine until my number came up to get the FC. A lot of folks have existing MIDI footswitch setups and use them. They're out there on the forum.
The new FC series switches are very tightly integrated with the 3, and provide a large number of awesome benefits that are not available over MIDI. The FC units' settings are all 100% assignable per switch and stored in the AxeFX3 unit. Each switch has a nice LCD backlit display to tell you what it does. Multi-color LED rings around the footswitch buttons to give you a visual indication of what classification of function the button does (i.e., bank, preset, scene effect, utility, switch layout, controller, etc.) for easy recognition from yards away. Stand-in switches that can make your external plug-in switches act the same as internals (minus the LED ring and label display), which is great for off-loading functions like bank scrolling/switching, layout switching, tuner acces, etc., to make room for more control switches on the FC to switch stuff that you want/need labeled & lighted. Each switch has two functions - one on tap, the other accessible after a configurable time-out when holding the switch down, so 12 = 24 (or if maxing out the add-on external switches, 16 = 32).
The FC has a basic firmware, but the functionality lies within the head unit, which means it should be a lot more future-resistant than the MFC. The FC controller pedal is nearly as awesome as the unit it controls, due to these features and its tight integration with the head unit.
Just look at it. Isn't this thing awesome?