yeah, i've noticed that. i also noticed how it takes forever to build a new planet when all you have is expensive high end stuff to put on to it. maybe a good alternative way around this would be two new game options. in Civ, you have to build a library to build a university. it's really annoying when an event happens that creates a new planet for you late game. when i'm trying to build up industry on a new planet and the only option i have is 'industrial sector', i can either spend a fortune, wait forever, or waste money cranking up social production for the rest of my empire. pretty bad options all around.
proposed solution: new governor and building options. it'd be nice if i could still build a basic factor when i've got industrial sectors developed. i can buy them cheaply. i can use them to to get a new colony's industry snowballing. it would be nice if you had to build the sectors in order, that way the development of a new colony late game would go fast, rather than slow. or what about an option to add an extra amount of funds to an individual planet's economy each year without having to go broke doing it upfront or financing? maybe add a 4th slider for "extra spending" or "diverted funds". whatever. check a box somewhere on a planet to mark it to receive the extra spending, which could work just like the hammer-and-shield points generated by industrial sectors (maybe it could also be put into reserach, i don't know). the extra funds are divided evenly among the checked planets. not too shabby.
regarding bringing back the saving of unused hammers, governor options could fix this. a simple "do not produce in the red" option could be added, and it makes sense especially since production goes to zero when you're in the red anyway. a more complicated set of options might be nice, too. there are what, 7 sector types that have upgrades? so add 7 options to determine how many of this structure type gets queued and built at once. famrs, diplomacy, morale and (less so) culture all remain pretty cheap. labs, industry and banks are pretty expensive. if you could set the AI to only work on a certain number of the expensive facilities empire-wide at a point, you could automaticlaly adjust how your economy works without too much micro management. if you say it's coming back, they probably all ready have a good solution, though.