I own a couple of each: 336 in .444, .35 Rem and .30-30, and 99EG's in .250-3000 and .300 Savage.
Both rifles have that levergun cachet; most people either love 'em...or not.
The Savage is available in flatter-shooting chamberings, not so much my two, but certainly the .243 and .284 Winchester. It USED to have the pointy-bullet advantage, but not since the advent of Leverevolution ammo. Also, since the introduction of the .308 Marlin, both can be 300-yard deer rifles.
I have found the Savages to be a shade more accurate, but only a shade. Marlins are far more accurate than many would believe.
For a truly traditional lever rifle, the Marlin has the tubular magazine and exposed hammer. The 99 has its own classic, but less frontier style.
I'm partial to both rifles, frankly, and see only the pros. Since either will kill anything I care to hunt, as far as I want to shoot, and are easy to load for, and get ammo for at Canadian Tire (at least the .30-30 and the .300 Savage!) I can't see a downside or any real advantage one has over the other. Both are pracical, good-looking hunting arms with a long history behind them.