If they don't want to rebalance the secondary stats, they could just do away with straight Agi/Str/Int gems and only have those stats as part of combination gems. Gemming would not be as mindless for DPS (just gemming your primary stat) and help balance out costs as different classes and specs have such different priorities for secondary stats. I'd rather see the stats be balanced, though.

As far as the enchanting mats, I think it's a good idea but one that could go horribly wrong in the short term. I do think that the market will be horrendously inflated early on as the initial flow of crystals will probably be slow but players race for world/server firsts and spend obscene amounts of gold to get an edge. After the initial blitz, though, prices should settle down and be much smoother across the market as a whole. I'm not sure how the current prices overlay with the new design (I think essences would be a lot lower and shards/crystals a lot higher, basing off of current dust prices being ~1g each), but a lot of it will just come down to what the market decides a crystal is worth as that high-end demand is likely to drive the rest of the market up or down accordingly.