I used to be a big CL lover due to the clean in tank look. On my 210 mixed reef I ran a hammerhead 5800GPH. It wasnt enough as the years went by so I slowly supplemented with a few tunzes a vortech and a mj mod until I had near 20000GPH to keep the ever growing SPS forest happy.
AS dragoneggs stated, there are pro's and cons to both.
In tank clutter, locline fittings take up much less space than powerheads. If you get enough locline fittings and possibly a penductor, they start to take up plenty of space.
Noise. Typically external pumps are loud where powerheads are quieter. My barracuda resonated sound throughout my house (a built in tank is attached to your walls so if its noisy its noticable in remote areas) I couldnt stand it. My wife didnt mind it. I didnt like the sound of the vortech I had. After removing my CL I had two tunzes and a controller. My house was quiet and I was finally happy. My wife hated the noise they made. Thats about when I broke down the 210 reef.
Power. Using a power calcualtor, @ 8 cents a KWH 24/7 for 30 days, 100 watts costs roughly $6.00 a month.
So a 350 watt hammerhead costs $21.00 a month for 5800GPH.
Two Tunze 6105's at 14 watts cost about $1.00
Cost. IME, with quality equipment, a CL pump, OM wave maker, locline fittings, doublu union ball valves, unions, PVC galore costs from $800-$1000 dollars for near 6000GPH.
A Vortech or Tunze wave maker system with about the same GPH cost about the same.
It all boils down to preference.