Bitterness from both seeds and skin is the usual arguement. I have never been able to taste a difference, but others swear they can, so maybe it is individual sensitivity, or variety.
I think deseeding by squishing out seeds before cooking will really impact flavor because the seed gel usually holds most of the flavor, especially tangy acidity.http://www.medicinenet.com/script/main/ ... ekey=55804
There are antioxidants mostly in the skin (flavonols), but unlike potatoes, which are starch storage organs with little nutrient value inside, and apples where only the flesh is eaten, tomatoes have fiber and nutrients throughout.
Just because the skin has some different nutrients than the interior doesn't mean that the rest of the fuit is worthless. The seeds are the most nutritious part, but you would have to grind them up in order to digest them because of the protective seed coat. That also begs the question about how available the nutrients in the skin are. I suspect that they use some nasty solvents not found in the human digestive tract when doing the extracting/testing.
Another option is to save the skins, dry them, grind them into a powder in your coffee mill and eat a pinch before eating the spaghetti.