Hi & welcome !
There's a plethora of built-in interfacing options you could use for prototyping, but since you are designing hardware and looking to do embedded development, you might want to consider coding your own I/O protocol from scratch - especially since you talk about "real-time".
In fact, you might want to consider patching FlightGear to remove some of the stuff (subsystems) that you don't need to improve its performance, and maybe get a little closer to your realtime requirement.
That being said, you definitely don't need to do any coding to get FlightGear to talk to other software/hardware - there's really straightforward I/O options like the AJAX interface or the props/telnet interface, as well as the XML configurable generic interface.
Ultimately it all boils down to your requirements obviously - and if you have a background in coding, i.e. if it's feasible to clone/patch/build SG+FG respectively.
I am sure we can provide additional pointers once you share a little more with us.
As a matter of fact, I am pretty confident that if you are interested in contributing back your modifications, there will be people really interested in teaming up with you - for instance, having a dedicated ARINC based I/O interface would be awesome to have for the project as a whole - especially for home cockpit builders and professional users.
Again, you don't need to do any coding to prototype things, but sooner or later it will come in handy if you have a working build environment to patch/rebuild FlightGear.
Not to mention, if FlightGear could provide out-of-the-box support for things like the "xVue Touch for Experimental Aircraft", that would be a terrific thing for the whole community