The Masada has a higher bore axis than the M9 (but what doesn't?)
The M9 has almost no useful texturing on the front and backstrap. The Masada does, although it could go further up the sides of the grip than it already does (to be perfect). Masada also has the removable backstraps with sides that extend forward about halfway along the sides; they're held on with a roll pin. The M9's backstrap has a long beavertail overhang that can get uncomfortable with a high grip and extended shooting sessions; Masada is more comfortable in that spot, for me.
The M9's trigger reset is very soft, the Masada's more noticeable. Reset distance is about the same. The trigger weights are comparable on mine, but while the Steyr has a short bit of gritty creep, the Masada has a longer, smoother creep.
The M9 has a mag release button that I always felt was too subtle... found myself hunting around for it more than once. Masada's, while a smaller button, is easier to find with your thumb (and it's ambi, so your trigger finger can hit it too).
M9's slide release is well-placed but relatively tiny compared to Masada's, which is large and easy to activate. Masada has front slide serrations the M9 lacks.
M9 has a stiff recoil spring and prefers hot ammo... occasional stovepipes have occurred for me with 9mm loaded to minor power factor (125gr @ 1000 FPS). The Masada has run everything I've put through it so far.
The tactical rail on both is about the same length but the M9 has only one cross slot to Masada's four (not sure if this has any practical advantage).
Both guns have an unflared mag opening not conducive to quick reloads. Both have baseplates which can be grabbed by the sides to rip out a stuck mag.
Both guns take down the same way (lock slide back, swing lever down, unlock slide, pull trigger to release slide)... though the M9 has the added step of depressing the safety button.
M9 has a notch in the barrel hood to inspect for a loaded round. Masada has a red-edged extractor that is supposed to act as LCI.
Masada mag springs are even more stiff than the Steyr mags.
Accuracy: I think the Steyr edges it out with iron sights. Speaking of sights, the Masada sights are serviceable but not the best. The rear sight is rather narrow. However, SIG sights are supposed to fit the dovetails, so you have a good variety of replacement options. With a red dot mounted, the Masada is accurate enough but not remarkably so.
The Steyr comes back on target quicker because of the bore axis. The Masada, out of the box with iron sights, had a noticeable case of trigger slap -- not awful, but there. That seems to have vanished when I installed a RDS, so I conclude the recoil system was designed to work primarily with a sight installed.
The Steyr feels tight and well machined while the Masada is a bit more loose feeling and the interior toolmarks a little more noticeable.
Do take note that the Masada has an interior chassis system like the P320, so you could theoretically toss the whole grip. I think this account for the relative bulk of the Masada.