It's all down to choice and I'll try and outline what I like about both.
TM Elite - Cheap no frills plastic rudders,that's not meant to be derogatory but they are cheap the act as rudder pedals and that's it simple as that no toe brakes but very good very reliable pedals. I owned a set that lasted me around 6 or 7 years before they died. Typical Thrustmaster rugged build that never gave me any problems, no drivers to install just plug them in and away you go. Nicely spread apart to feel realistic but not spread too far so you feel like you're at the gynecologist

They interface perfectly with the Cougar and plug directly into the base of the joystick and the Cougar and pedals are seen as one device so even older games can take advantage of this great rig.
CH USB Pro Pedals - More expensive than the TM Elite's but come with the added extra of toe brakes. The rudders slide up and down as a normal rudder pedal set would and each pedal also tilts like a car pedal and infact the pedals come with stoppers so you can stop the rudder action so you can use the pedals for driving games (although I prefer dedicated car pedal sets for driving sims) The usual good CH buildquality on display again in these rudder pedals they feel very solid even though they are made of plastic like the TM Elites. You will need another USB port for these pedals and that means Windows will see the rudders and Cougar as TWO separate devices which means older games which only supports one controller will not see the rudder pedals. Such games like Falcon 4.0 and Flanker 2.0 will not allow input from more than one device. One newer games such as Aces High, Warbirds III, IL-2 Sturmovik these pedals work great! and the added toe brake facility is very handy in Aces High for taxiing to the re-arm re-fuel pads and taxiing from hangars. A very nice set of pedals.
Both rudders have great build quality and it's hard to pick between the two. The only real problem comes if you want to play older games like the ones I mentioned above (and many others) that only allow input from one controller. Another downside to separate rudders that don't plug into the Cougar is that you won't be able to program the axis of a separate device but you will be able to plug any rudders that connect directly into the Cougar. I have both sets of rudder pedal and tend to use the TM Elites more than the CH ones.