Its true, when you look at the base chassies, they are remarkably close. Both have roughly the same amount of pod space (38 for the Night Gyr vs 35 for the Flamberge) almost the same amount of armor (the Gyr has 5 points more, with slender advantages in all torso sections, with the Flamberge havng more in the legs and on the rear) the same amount of fixed equipment (4tons of jets vs 3 tons of SRMs, and the burden of finding room for ammo). The Flamberge does have a bit more pod space (standard armor is used, and the SRMs take up fewer crits than the JJs, though the Night Gyr does win back with one more fixed sink). There's not one catagory in which one side is fully better, and each has its advantages.
The reason I see the Night Gyr as the clear choice, though this is for my fighting style and the way I like to get down, and not in terms of overall utility which is harder to mesure, is because of how the veriants went. The two main combat versions use either 12 or 10 tons of IJJs, leaving too little room to mount a really blistering arsonal. The Prime is a nasty infighter, with four MPLs, two ATM6s, and two SRM6s. But that compaires closely with the Night Gyr E, which has six MPLs, just one of each SRM and ATM6, but an extra two LPLs to make up for its lack of mobility. If its me, I'm betting on the extra fire power (pulse power in this case, which is helpful here) to trump and extra 2 MPs. The Flamberge A is a bit harder to match, since the Night Gyr lacks a TC/Pulse veriant, and the Night Gyr's own TC veriant can be cheritably refered to as problematic, with its three Ultra2s. Even then, that C veriant can match Quinn Kerensky's ride for power at range while adding even greater range (the longer medium brackets on the Ultras can almost make up for the lack of pulse mods, though they're still two point plinkers even then, accurate or not) and its got much better heat managment, alowing it to keep up a more sustained fire. The Night Gyr lacks fancy artilery or anti armor veriants, so its harder to compaire the other two, but the B with its Ultra 2s makes a decent tank hunter and offers comperable over all power with the GRs, and you can always just take the Prime or A or D and just blast enemies into oblivion by pure power, which the Flamberge can't really match.