Note: I make some rough criticisms, only because I like the game a lot. If you dont believe me, read my love letter to SD in the last paragraph 
I am NOT an advanced player but since GC1 I have been wondering why stardock had done it this way. It makes it harder to balance the budget since you do not allocate a certain amount of cash to production. Instead you choose a sum total percentage at which you want to drive all 3 of your industries. Then you break down that percentage among the 3 industries.
It gets a little funny with research because maximum research capacity is determined differently from max military or social industrial capacity. One reason for why the sliders operate on % and not on money is if your industrial and research capacities are mismatched, it would be possible to allocate more cash to one department than you'd be capable of putting to use. For example, your industrial capacity is 500 and your research capacity is 10. If you were to split the -money- fifty-fifty, chances are you would be allocating way more to research than it could make use of. Then whoever designs the game would have to decide if that money should be wasted or unspent, should the player be notified and how, etc.
So that's why it works the way it does. But i'm not totally happy about how it does work, because it makes for some improbable scenarios. Let's say you have 500 industrial and 10 research capacity, and the main industry slider is at 100%. If you want to go 50-50 on military and social, the reasoning works like this: "OK, we're using 250 points of industry for military and 250 for social. We can't put any more points toward military without taking away from social because military and social draw on the same industry resource." Makes sense. But what if we go 50-50 between military and research? "We're using 250 industry points for military and 5 research points. Those other 250 industry points are sitting idle. We cannot use them for anything. If we want to bring those other 5 research points online, it will cost us the 250 industry points. Maybe it's because of a manpoiwer issue, but then again if we had twice as much industry, we would still be wasting half of it."
The second scenario bugs me. The restriction in the first scenario makes sense because the military and social APPEAR to be drawing on the same resource (industry points). The second scenario shows that the common resource between all 3 categories is actually the PERCENT UTILIZATION of ALL INDUSTRY, which must be divided among all 3 industries. Doesn't make sense to me.
I do NOT claim to understand the game better than SD, but from where this n00b sits I think it would make more sense or be more intuitive if you were able to drive the research industry independently of the military/social production industries. And bringing in some of the above questions from other posters, I think the lack of transparency as to how the figures are calculated makes it incredibly hard to understand AND debug IF there were a bug. (My favorite analogy, building a car without a dashboard...) Remember in MOO2 how you could click on all the hammers and see exactly how it came up with that number of hammers? Well GC2 does NOT have to be like MOO2 but help us understand what these bonuses and stuff are really doing 
What we have now is that you research a new type of factory/lab, the game automatically upgrades your facilities, and since you set production by PERCENT and not credits, the game goes on using the SAME percentage of a LARGER capacity, which costs more money, and the budget gets broken, slowly and insidiously over the course of a dozen turns while the facilities are upgraded, all because you researched the next level factory. Shame on you, don't ever research anything again.
I would argue that the decision of how to allocate resources depends on what resources you HAVE, and your policy of saving / deficit spending takes priority over any kind of decision like "we should spend equal amounts on these 2 categories". GC2 does NOT allow you to manage this way because the TOTAL spending value changes as you muck with the resource allocation sliders. I think SD has already caught onto the problem and tried to address it with the 'focus option' (which, by the way, we have no way of seeing exactly what it is doing ). The problem in GC1 APPEARED to be that all your colonies had to be doing the same sort of production (military or social) or else your allocation was wasted if you went 70% military but only one colony was actually building ships.
For anyone who miraculously is still reading this post, I think this is how it should work: There should be 3 sliders total instead of the 4 we currently have (overall industrial drive %, military%, social%, research%)
1. Industrial drive slider, sets a number of credits to spend instead of a % to drive the industry. The minimum is 0 and the max is what it would cost to use all your factories at maximum. When you build new factories and the max value goes up, or you lose production abilitiy and it goes down, the SLIDER AUTOMATICALLY MOVES so that the same number of credits are being spent until you actually make a decision to spend more/less by moving the slider.
2. Military/Social Industry allocation slider, decides how many of the credits from (1) go to military and how many go to social. Push it all one way for all military, all the other way for all social. Slider never moves automatically. Of course, to make the game accessible, we always display how many credits are being spent on each category.
3. Research slider. Remember in my fantasy world, you can set factories AND labs to work at 100% if you have enough money. Minimum is 0 and maximum is the cost of driving all research at 100%. Again, this works in credits similar to (1), and again, the number does not change until the player decides to increase spending.
Put these 3 controls somewhere on the main game screen if necessary, so the player can keep up by adjusting spending as capacity is changing... shouldn't take up too much space but make it hidable if it does, e.g. the FIND button is kinda huge
2a. If a colony does not have a military/social project, do NOT waste the money. Dump it all into military/social if one type of project doesnt exist. Dump it into research if neither project exists. If research overflows, return it to the treasury. I have no idea if money gets wasted in GC1 or GC2 (blame the UI for that
), but this SHOULD NOT happen in these games only because the game does not provide the player with a warning or a means for tracking it down and eliminating the waste.
Has the following advantages:
1. Lets the player decide how much to spend each turn, so that you can save/spend your treasury without having the game move the budget all over the place.
2. Removes the artificial trade-off of spending 100 credits to power 10 factories in exchange for 10 credits to power 1 lab (or vice versa).
3. Much easier for new players and non-mathematicians to understand what the game is actually doing with the money
4. No fear of economic upset or a dozen turns spent rebalancing the budget when you research a new type of factory or lab (now, on the other hand, Farm upgrade technologies are actually suggested by Dread Lord espionage agents posing as scientists )
5. Fewer UI elements (always a good thing)
YES I know this would mean redesigning the game. Not asking for that. Just posting it here to see if anyone agrees with my way of thinking, and so SD gets a good jump on doing it my way for GC3 (kidding... sort of.) To reiterate, SD has done a fantastic job and has set an example for all other companies to follow, hopefully GC2 will be a great success and other companies will be shamed into dropping the sleaze act and following SD's example on how you really make money in the gaming industry. Here's hoping.
GalCiv2 Forums
Stardock Forums
I actually like % better. Because usually your % is about the same through the game. You build new improvements, but you also have more taxes. I often in GC2 put spending to 100% and do not worry about spending at all. Instead I try to build only the staff that I need.