1) Trinkets are valued for CMs based on value/itemlevel (up to 463), and the best "bang for your buck" trinkets we've seen are the ghost iron dragonling, bottle of infinite stars, and the relic of xuen. None of the newer trinkets bring more DPS per ilevel.
2) Mastery was WAY ahead in 463 gear (FOR ASSASSINATION), and should be treated as such if you're optimizing your gear - combat, of course, still favored haste.
3) Absolutely - every time ilevel goes up (specifically on items with sockets) there's a function of the "squish" that allows for a slight upward trend - 549 gear with gem slots will reward you significantly more stats than, say, 476 gear, although in theory they're intended to be equal. Hit the hit cap (and expertise if you're going combat) for level 93s, pump mastery (or haste for combat), and get as many gem-slotted high-ilevel pieces on as possible.