Bubbles from a skimmer might unfortunately be a fact of life, this is why they are typically run on sumps instead of the main display. Doesn't solve the problem but makes the symptoms go away..
I personally would adjust the skimmer so that it's running optimally for you. Throttling back water flow or air flow will just mean less skimming .. right? So what I'd think about is maybe some kind of bubble trap. A small acrylic box with an overflow might do the trick. The skimmer empties into this box, the water has to overflow the box to get back into the tank, and in so doing, most if not all of the bubbles escape without getting into the main tank.
If you're not into an acrylic project, a piece of larger diameter PVC capped off at the bottom might work. The acrylic will be prettier, though.
What some skimmers do, is combine this box into both intake and outlet (separated into two separate compartments) so that you get the benefit of surface skimming as well.
HTH
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-- Tony
My next hobby will be flooding my basement while repeatedly banging my head against a brick wall and tearing up $100 bills. Whee!
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