Is it the.... Imperial federation or something?
Never played with them, but I think they focus on Influence (the purple star). Don't know what they do with it.
What determines this score of 146?
An average of everything (population, FIDSI, military, wonders...).
I generally wouldn't focus on the score too much, especially at the beginning since the AI has special bonuses at the start to help it cope with the game. Midway-through, it becomes a good indicator to see if you're behind. It's also useful when picking on a neighbor: since all the AI have the same starting point, you can infer the ones or top are doing better than the ones at the bottom.
How do I use these resources?
Right now, you can't. However, you will once you will be able to develop your system (something that happens when you develop the Economy segment).
You will see it in the (currently) big empty space below the highlighted square.
It's something that is not really well explained and I often miss it, but basically... The science tree is divided in 4 sections, themselves divided in rings. When you reach a different ring of a section, you get a few free stuff, on top of the possibility of researching the technologies of the following ring. You often need to decide whether to keep going forward into the tree for the more expensive but potentially powerful technologies that will allow you to advance further, or stop and get the technologies from the previous ring because you need that specific thing now (also, each technology you unlock raises the cost of the following ones by a few percents, regardless of which ring they're from).
And one of the benefits from the right quarter of research is "Empire modification". It's super badly signified and I often forget about it for several turns, and then suddenly I open the economy screen and I discover I have 2 empire upgrades to decide upon.
What it does is that you can select to use one (and then two, and then three) luxuries to upgrade a system. The bonus you get depends on the luxury you've used. Once you've decided that, you'll be able to build in each system an upgrade that costs Industry and the luxury(ies) you've selected, and it will give quite a few bonuses to your system, on top of the bonus the specific luxury gives. You probably won't have enough luxuries to upgrade all your empire, so you need to focus on your better systems and upgrade them (especially since you can't upgrade a system to level 3 if it's not at level 2, so you need enough resources for level 2 at the very least).
In general, I'd say it's not necessary to hunt for specific resources and just upgrade with whatever you have at hand now (because it becomes quickly expensive, and you want to do it with whatever resources you generate naturally). However, if you have resources that don't align with your needs (+ food resources on an empire that doesn't eat) or you're really focusing on something right now (you play the science empire and you really only want science), then it can be a good idea to wait until you get a few systems that give that resource. Remember that whatever you select there will only be active quite far down the line (once you've built it on enough systems to make a difference) so you need to think about it long term. Don't pick Dust generation because you need money now, because it won't give you money now and will only start to give money back in several turns with some possible expensive improvement.
Is it possible to choose buildings for each planet independently or does the game do for everyone at once?
Every improvement is system-wide, not planet-wide. At some point, something will appear below "colonized": that will be the "specialization" of each planet (this planet will produce one more science if it's cold, this planet produces 2 more food if it's fertile, etc). That's the limit at which planets can be differentiated from others in the same system.
(You still need to individually colonize them when you unlock the technology for them).
I completed this mission but it was by accident.
It happens often! Some missions give good enough results or are easy enough that you may want to change course and complete them; some others give shit you don't care about or require far too much investment/micro-management and you're better off focusing on building better military/science/industry buildings.
If you want to follow the scenario, you may want to try to focus on the scenario missions (as finishing the scenario of a faction leads to victory), but it's often easier to win in the traditional way of genociding most of the galaxy/owning so much money that nothing else matters.
