Hahn, we have both types of bubble plates, the many smaller holes and the fewer larger ones. We are currently using the many/smaller one and get good results. It was reported to use that we should try out the fewer/larger one because several people had better skimming when using it versus the many/smaller plate. I cannot say myself from personal experience, but just wanted to pass that long.
I can speak to the lid also, but again only based on our lid. I have seen no problems with the holes leading to the carbon filter getting clogged with foam and/or skimmate, but our lid has the carbon chamber on top. I think the one you looked at was a special order/design for clearance reasons where the skimmer was going to be set up, but I really don't know
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I am not sure how I feel about the inlet pipe, but it is something that Scott and I discussed on several occassions. We do have ours turned to the side so that the inlet water doesn't go straight down, but does "spin" a little (reminds me of our old Deltec 902 in that manner).
Since we got our water level tuned in on our skimmer, and it slimed up sufficiently, we have had great success with it's efficiency and the wattage draw dropped a solid 15w (since it slimed up), which I found interesting, although it does make sense.