I'll second the request to see the formula, but I understand the intent in not revealing it.
From swapping gear in and out and looking at the change in my score, I've concluded that there might be something off with how gems are counted. Compare Shiver
, for example, both ilvl 232 tanking weapons. Shiver has a socket, but has 1 less Str, 8 less def, and 6 less hit. The socket, with a rare level gem inside, counts for approximately as much as the deficit, without including the socket bonus. From this and other examples, it is reasonable to conclude that sockets are already accounted for in ilvl: a 232 with one socket is equivalent to a 232 with zero sockets in terms of itemization budget, when it is assumed that a rare gem is socketed.
The problem is that having a rare gem seems to confer a point bonus, where really it shouldn't confer any bonus. Epic gems should confer a bonus, and gems worse than Northrend rare gems should confer a penalty. Perhaps even instate a penalty for not having a Stormjewel. Similarly, if someone is a Jewelcrafter and has 3 JC gems, they should get a different point bonus, equivalent to that gotten by a tank with max Mining, or a tailor with the cloak enchant, or an enchanter with two ring enchants, or a blacksmith with both bracer sockets, etc. Score gain from professions should be streamlined, and score gain from gems should be correctly related to ilvl.
Then, it could be argued that socketed items allow for better itemization (more of your best stat, less of the crappy ones), making them better in general. This is somewhat true, with socket bonuses contributing somewhat, but the exception is that a socketed item may for example be very heavy on Stamina or some other useless stat, and a non-socketed equivalent may not. But if the discrepancy of sockets vs no sockets is currently taken into account, then the gain from socketed items over socketless equivalents is probably too high. Of course, I could be wrong about rare gems conferring a bonus in the first place, but I thought it was worth mention. And I'm sure you won't reveal the formula, but in the case that you hadn't considered any of that, it might help.
Enchanters, Tailors, LWs, Scribes, and maybe Engineers should get a boost to their enchant scores; Miners (who are also tanks), Alchemists, and Skinners should get a separate bonus; Blacksmiths should get a bonus a la the belt buckle for each extra socket; and JCs should get a bonus for each Dragon's Eye they have on. The maximum bonus for each profession should be the same. (Herbalism should not confer any bonus, as it's not useful for PvE.) This way, raiders who worked hard to get two professions that would benefit us in PvE will see that effort reflected in our score. (The JC bonus should perhaps be slightly higher than the others because it's OP, at your discretion.)