Passinglurker: A complete (thermodynamically accurate) generator overhaul might be a possibility, but would be quite a bit more work than simply fixing the nuclear reactors. I'll consider it if I have time.
Misticblade: Yes, crafting nukes will be altered. You'll be able to choose between gun-type and implosion-type warheads, with varying yield based on isotope and enrichment level (protip: plutonium's spontaneous fission rate is too high to be used in a gun-type device!). Multi-stage Teller-Ulam warheads will also be craftable.
Lazurkri: The improved mining laser would likely have an "Anti-Organic" mode - a high-power, low-focus system ideal for scorching a large cross-section of flesh - to burn mobs without affecting terrain. I'd also like to make the projectile strike instantly, if possible.
Krazygluon: I haven't included Buildcraft compatibility yet, but it's on my to-do list. Eventually you'll be able to suck used cells out the bottom of the separator - and the fusion reactor will accept fuel and lithium, allowing a fully-automated fusion setup.
Something else I've been working on lately is a cloning machine, scheduled for release soon after the defense update and compatibility patch. Ever wanted to copy your seeds, grow dozens of Spawn Cat eggs from a single Siamese's DNA sample, or even build your own Creeper factory? The fabric of life itself is your plaything with the Rocket Science Cloning Kit (nutrient paste sold separately).