Tossing the component groups against each other, the Cobia's Sram X.5 shift/deraillerus is superior to the Alivio componentry in responsiveness to the casual rider, however, if you were to pick up either bike and start riding it, you'd have a bike that shifts well in itself. Each has basic hydraulic discs, I'd consider this a wash. The Cobia does have a 10 speed drivetrain, the Cannondale has 9. Many new drivetrain sets are moving to 10 speed (X.9, XT, etc), so if you were to upgrade, the 10 may suit you better and wouldn't require a new chain, cassette. The Cobia's fork (Recon silver), however, IS a significant upgrade of the Cannondale's Deuce, as the Cannondale SL4 doesn't quite his the pricepoint to employ the fatty/headshok or Lefty that the cannondale's are build on. Upgrading forks for cannondales is also a bit expensive, as you need an extra headset reducer and new stem. Then you have a weakness in the headset, as the reducer isn't a sealed ball bearing (sorry, a bit techy for the question).
HOWEVER!!! The Cobia's frame doesn't touch the Trail SL with a 10 foot pole as far as weight, rigidity or upgradeability. They also have extremely dissimilar geometries (if you have long legs, Cannondale's for you, if you are more of a longer trunk person, Fisher would fit you if you are comparing similar sizes). The Cobia has a more forward facing, aggressive geometry, where the Cannondale may be a bit more universal.
If you are doing a LOT of offroad and don't want to get into upgrading and use your bike as is... go for the Cobia. The Cannondale could be a tad better at that pricepoint. I'm seeing some Cannondale Flash 29ers out there pretty heavily discounted... now that would be pretty unmatchable across the aluminum market. Hope that helps!!