Advanced materials can only be melted/alloyed in a tier-two smeltery, having higher melting points
T2 blocks replace nether smeltery blocks
Worldgen
BuildCraft oil spawns have been redesigned
Biomes fall into one of four categories: "Full", "Common", "Scarce", or "None"; only the first two can spawn buried deposits and the majority of biomes fall under "None"
Every position in the world has an additional 'richness' multiplier to control oil spawns; even in appropriate biomes, most areas have a richness of zero
Buried deposits have been redesigned; they no longer have spouts, and are larger, much more convoluted in shape, and will avoid ores, caves, and other non-stone blocks (click here for a rendering of one in diamond blocks)
Buried deposits, being invisible from the surface, must be found via mapping tools like the RotaryCraft Ground Penetrating Radar
Cave systems will generate occasional chests with early-game mining-focused items, such as ore, tools, torches, and food
BoP firegrass will spawn in patches in soul sand
ThaumCraft crystal clusters will occasionally spawn on cave walls
Small geodes of "Lensing Crystals" will generate deep underground, hidden in stone, and require special tools to find
Strongholds contain...rare secrets
TiC oreberry spawn redesigned; clusters are rarer, larger, will only spawn in larger cave areas, and will never overwrite other blocks
Bees
Carboniferous Bee
Produces oil products
Not bred, but instead reconstructed from salvaged DNA
RNA fragments are extracted by centrifuging oil and then reconstituted into a complete genome
Gaia Bee
Produces Gaia Spirits
Requires Gaia Pylons and a mana supply
Curative Bee
Produces sano beans
Has a rainbow-tree like ambient effect
Twilight Forest bees
Glowing Bee - produces TF torchberries
Live Bee - produces TF liveroot
Shrouded Bee - produces TF fireflies
Carminitic Bee - produces Carminite and redstone combs
Essential Bee - produces crystallized essentia
Wispy Bee - produces wispy essence
Tainted Bee - produces tainted goo and tendrils
Hexahedral Bee - produces hexorium crystals
Fluffy Bee - produces fluff, melons, and cherry leaves
Transformative Bee - a bee with mysterious effects and yields
Other
Added an NEI handler for engine fuels
Added an NEI handler for fairy lights recipes
Added an NEI handler for hexcraft fuels
Added warning when world save is disabled
Added custom mystcraft pages for unique worldgen features, including non-shadow-casting floating islands, oil caverns, no mob spawns, no leaf decay, and no fire spread
Added custom mystcraft instability effects, including TNT rain, fuel inefficiency, and unbreathable air