I was considering whether or not I'd go the TC3 route, in regards to research. I'd definitely love to have a book that basically acts as in-game documentation and reference material that you can pick up and use without ever having to switch screens between Minecraft and your browser.
I may make a compromise between TC3 and regular "craft it, given that you know the recipe" systems. Like, some things are fairly obvious: heating water makes it boil and steam can drive things like turbines to make electricity. I may go a step further and hide some recipes in NEI, but make them still useable from the get-go if you know 'em, like the elemental arrows and such; they're a relatively simple concept, but not readily obvious.
However, I do like the idea of a kind of rudimentary scientific/mystical research, where you can put certain things in like, say, oak saplings, and attach your research desk to various machines nearby to see how saplings can be used and/or processed, which can lead to discoveries like bio-lubricants or combine them with mystical research on earth crystals and discover, say, a block that'd increase crop growth speeds...maybe even increase their yields, so you could have something like a Fortune effect in a certain radius around the block (maybe...9x9x9 or so?), but doesn't alter their fundamental mechanics, allowing normal automation to proceed unhindered. Sengir's done something similar with grafters, they give you a large boost (dunno if its 100% or not, though) to your chance to get saplings from breaking leaves, so I don't see why it couldn't apply to things like apples or wheat.
[ETA]
Prolly tooting my own horn a bit, but the more I look at it, the more in love I get with the idea of true class in Minecraft. Thaumcraft comes fairly close, but its all got an arcane feel to it, more along the lines of something you'd find in a mage's tower, and not in, say, a lord's manor. Hell, I'm tempted to have an entire module dedicated to JUST adding a ton of class to Minecraft: area rugs, carpet, decorative chairs and thrones, actual tables, chandeliers, crystal/gold goblets, dining plates, candelabras, sconces, just...a TON of decorative (and maybe some functional) luxury items you can place in the world. Turn a simple base into a manor fit for a king, so friend and foe alike can come to your home and stand in awe of its splendor, refinement, and luxury.
Lord Steve of Minecraftia, your manor awaits.