Here are some suggestions I've been thinking about for after GT5's survival features have been fully implemented.
These are the little quirks that can really enhance gameplay:
Tooltips: The simple addition of tooltips over the buttons in GT machines could be incredibly useful.
Crafting and Multiblocks: I think that the use of machine casings in-world, making more multiblock machines and therefore decreasing the number of crafting steps for a particular machine would force the player to rethink the basic "wall" of machines. Essentially, instead of using, say, iron blocks in a machine recipe, you would reduce the number of crafting steps and make the requirement of 26 machine casings and a bucket of water in the middle.
TFC-like Prospector's hammer: Make the GT hammer more relevant as a proPick, possibly by being more accurate but with a chance of false positives. Higher accuracy, less precision.
Bigger Changes
Focus on Fluids: Use the wonders of 1.7 Fluids to add fluid byproducts, which can be pumped and processed and all sorts of fun things.
Less GUIs: Minecraft is a game that focuses on in-world gameplay. GT has so many GUIs that it would be nice to, say, craft things, or use machines without the use of GUIs. Take mods like TFC, Botania, Thaumcraft, Industrialization, Resonant Induction... all do really well with more in-world content.