From a purely functional standpoint, don't bother with a dedicated reservoir. Your system would be every bit as effective (and smaller) if you merely used the same tubing for your "reservoir" as you have inside the case. I suspect you want the reservoir larger for a few reasons including:
1) Air trap
2) Fill/drain/bleed location
3) "Looks"
4) Perceived benefit to cooling
You don't need #1 if your system is sealed well and you have a point for bleeding air. You can do the first parts of #2 with a T in the line. Number 3 is completely your call. Number 4 is not applicable as a reservoir does essentially nothing for cooling.
All that said, if you wish to have the reservoir as you've described then it should not be too hard to eliminate air bubbles. Air bubbles have a tendency to rise to the top at a predictable rate. This rate is on the order of 3 feet per second (going from memory here, but should be close). So long as your reservoir runs nearly full and your downward velocity is low enough, the bubbles should not reach the pump intake. A 2" diameter will keep the velocity low enough so long as you don't "drop" the water too far at the top. The other option is to place a baffle in the tube. This is nothing more than a roadblock to break-up a flow stream that is not uniformly distributed. A stainless steel screen does nicely.
If your aesthetics allow, a submerged return would be even better at preventing air entrainment. All depends on what "look" you're trying to achieve.
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