In order from more-likely to less-likely:
Hoses. Goddamn, we can explore the whole solar system, but we don't have hose technology? Especially with the addition of stock ISRU. Using the klaw for ground ops is a pain in the behind.
As someone who loves the NERVA engine, I would like to see a set of 2.5m LF tanks. Having to use the LFO tanks minus the O is really frustrating, seeing as how ~half the volume is totally unused. Sure, you can make do with the Mk2/Mk3 LF tanks, but they don't quite have the same looks as the cylindrical 2.5m parts. On the topic of nuclear parts, a 2.5m NTR would be nice, something with a decent amount of thrust. Of course, a gas-core nuclear rocket would be a fun end-game motor, but that may be a little too speculative for the devs to consider adding.
Movable parts. I don't have any experience with mods that do this, but having robot arms and cranes would seem make base construction so much better.
More minable resources and some new resource converters. Minable ice / pumpable water for electrolysis, collectable CO2 for NERVA use, plant growth or conversion in to methane, different grades of ores to return different materials. Probably not practical until the life support update, which will put a much larger strain on consumable resources making ISRU necesary.
Something that might be nice, that I haven't seen anyone mention yet would be radiation. This would probably go alongside a life support update because we would need a system for tracking the status of individual kerbals (food, water, sanity, acute / lifetime radiation doses etc.). Something akin to Van Allen belts around Kerbin and Jool, solar flares and cosmic rays, and the NERVA should be radioactive in some form or another. This would limit the utility of the NERVA to orbit-orbit operations. A variable-radius shadow shield would be a necessity, as well as some form of medical bay for reducing the effects of radiation poisoning. Remember, water has a great HVT so that could provide radshielding as well. Perhaps a set of standalone nuclear reactors as well?
Ideally I would like to see trojan points, but that has seen a bunch of discussion recently and given how KSP's physics works that is probably a pipe dream.