A lot depends on what you're used to for flight sims. I played the first X game back when it first came out (1999) using a mouse and keyboard, and I found that it worked really well. I had tried it on a joystick at that time, but didn't like the feel.
I've been playing these games again recently, and didn't even consider using a controller or joystick, but my control came right back as soon as I had on hands on the M&K. So mouse and keyboard are definitely viable if that is your preference.
It is worth noting, though, that by the time of X I had been a pure PC gamer for many years and hadn't used a joystick regularly since the '80s (Atari 2600). If you are both a PC and console gamer, or if you're used to using joysticks on PC, you might well find that control scheme preferable.