I had that same experience when I first got my 330SS . . . I felt my 242SS ran better in the chop . . . well, it probably does.
The 330 SS has a fairly flat hull ( 20˚ V) vs. the go-fast boats and large center consoles (24˚ V). So, depending on what you are used to previously, it can be a big difference.
What I found is that you have to put the bow down into the waves/chop to get a good ride. The more 'pointy' section of the hull (bow) will be cutting into the waves rather than the flatter part of the hull pounding the waves. Of course you are limited to about 3 footers as being the maximum before you will want to slow down and keep the bow up a bit, otherwise you run the risk of a 'nose dive' as the waves get bigger . . . like 4-6 feet.
I would trim the boat using mostly the outdrives, and the boat seems to like to run with the outdrives almost in their full down position, but not quite, just a little bit above full down,
In a 2-3 foot chop, I can usually hold 25-28 mph. If things get rougher or there is a rouge wave, I just try to keep the boat level while airborne.
Overall, I'm not in love with the ride, but I've learned to live with it. The newer Sun Sports (290, 310, 350) have a slightly sharper 'V' hull, so presumably those boats ride a bit better.