Here is a revised design. The bottom of the reservoir is bellow the water level of the tank, so the siphon will remain primed. The outlet of the siphon is turned to the side to limit substrate disturbance. It could be pointed at an organism that likes periodic current (maybe some type of coral). In the event of air getting in the siphon, an air outlet is situated to allow air pockets to be forced out by the rising water. A 1-way flow valve, like those used on the airlines from an air pump to the aquarium, prevents air from re-entering the siphon. Surge Filter Revision A.jpg
Here is a close-up of the air outlet: Surge Filter Revision A Siphon.jpg
This has the advantage of allowing the system to recover from a siphon failure without intervention from the owner. Also, it will self prime. For those more electrically minded, it may be easier to use a float switch to turn off the pump if the reservoir level gets too high.
The volume of the filter is not intended to be too large, maybe 5% of the total system volume at most. This should allow for rockwork and pumps to be near the surface, just not directly at the surface.
I think this covers all of the mentioned design flaws. Did I miss anything?
P.S. I didn't take any of the criticism as negative, bearwithfish. Constructive criticism is always appreciated.