Well, I hope with this guide I might help make going through the Starbase system more fluid and an easier pill to swallow. There are a few points I'd like to start with before I get into the guide proper:
1. It's still just a game, and it's not going anywhere. Try not to let yourself get discouraged or frustrated over the SB system. Put it aside for awhile, maybe even play something else. Time is on your side for doing this.
2. This guide is not perfect. I'm not trying to make an 'all encompassing' guide which will work 100% guaranteed no matter what. If you don't agree, that's alright to me, I knew going into this that I simply would not have a guide that would be liked by all or completely usable for all fleets. This guide is also not meant to be a guide to actually running a fleet, because there are simply too many ways that could happen; it's focus lies on the actual leveling of the fleet holdings and such.
3. This is not going to be a short read. Might be good to not read this whole thing in one shot if you don't have a lot of time.
4. Here's an important one: The fleet system is designed around 25 people (not characters or alts, actual accounts) playing at a fairly regular pace. So try and keep that in mind when reading this, and perhaps adjust some of it accordingly based on your fleet size.
Ok, now to begin:
Section 1: The Fleet Advancement System
The Fleet Advancement System was something introduced with Season 6. This introduced the Fleet Starbase as the first, and primary holding. Season 7 introduced the Embassy, as the first 'Outpost', which is a smaller, secondary holding that is cheaper and quicker to build as compared to the Starbase. As time as gone on, more of these similar outposts have been introduced, and will probably continue to be..
Each holding is made up of various areas which you fill projects to gain experience for, and then 'level up' through various tiers. Every tier improves the look of the holding in some fashion, along with unlocking various things for the fleet to buy.
There are two areas for projects: Normal projects, and Special projects.
Normal projects are your primary means of gaining experience in the holding. These projects include for each area: Basic provisioning (dil cost only), provisioning for X, a 'pure experience' mission, and also possibly a 'lesser experience' mission.
Special projects are Upgrades and Special projects. Special projects (for the Starbase only) are designed purely for the sake of allowing larger fleets to give more people more chances to gain fleet credits. All special projects like this also only give a very small amount of experience as well.
Featured Projects are also slotted in the special project slot. These add to varying degrees enhancements on the inside of a holding (such as opening the shutters on the Starbase, adding a fish tank, and so on).
Upgrades are generally the most important, and most expensive part of the holding to upgrade. These are divided into three as well: Individual tier upgrades, overall holding upgrades, and special upgrades.
Individual tier upgrades are important because they are what you need to continue advancing in an area of a holding. If these upgrades are not completed, you are locked out of most missions in that area until it is done. Overall upgrades are the most expensive upgrades of all, because they are what enhance the main area of a holding (Starbase itself, or the Embassy, and so on). Special upgrades are cheaper compared to most other upgrades, but add other unique services and conveniences, like allowing a Bartender on the Starbase.
Section 2: Starting from Zero
Now, for the sake of this guide, it will be as if you are just starting out.
To make a fleet, you and 4 other people must be on a team together, and go to the person who can make a fleet on Qo'nos or ESD. It's a fairly simple process. Once completed, you and your fleet should discuss what is actually wanted by everyone.
Try and steadily narrow it down until there's an agreed upon choice. A few points I'd like to recommend though:
1. If focusing on an Outpost, do note that Outpost Provisions (called 'Embassy Provisions' and similar names for other areas) are gotten from your replicator and cost Fleet Credits to make, not normal Energy Credits. Also, they are cheaper based on your Industrial Fabricator on your Starbase.
2. The Starbase itself starts out at tier 0, and it has hull and shields, but otherwise cannot defend itself in the PvE missions of Starbase Defense, Fleet Alert, and Blockade. So it's a good idea to at least get it to tier 1, so it can shoot at attackers if you ever do these missions.
3. Going on the above, leveling up your science area can be an excellent means of doing that, because after you upgrade the Communications Array, you will be able to upgrade the Transwarp Gate to tier 1, which will give everyone in the fleet the option to transwarp to the Starbase.
4. Upgrading everything to tier 1 is useful, simply so you have access to all the basic facilities, particularly so you can begin provisioning missions. This isn't required, but it is very useful to have. Also, once you get an area to tier 2 on the Starbase only (such as the shipyard), you will be able to buy common DOFFs of that area (tac, eng, sci) from the DOFF guy on the Starbase, making it easier to fill projects of that type by spending FCs to do so. I will explain a bit more about that in the next section.
Section 3: Projects
So now that you've begun working on an area, it's time to slot some projects. At tier 0, your choices are pretty few, but once you've gotten an upgrade done and out of the way, your options open up a lot more. Projects generally need a mixture of the following:
Data Samples/Particle Traces
The first five are pretty much the staple requirements. Outpost Provisions are needed on all the various Outpost missions, Data Samples/Particle Traces are mostly for the Science area on the Starbase, and Other refers to things that aren't used as much or used for certain things (like buying a lot of 'Food' and 'Drink' items to get a Chef on your Starbase).
Here's some ways of getting each of the above:
Fleet Marks are gained in a large variety of ways. This includes, as of the time of writing this guide: Fleet Action Daily (one of three), PvP Daily (one of three), PvE queued missions, Officer of the Watch Daily, Duty Officer turn-ins, and the Deferi ground adventure zone. This guide itself won't be going over any of these things individually, but feel free to ask and I will gladly help out.
Dilithium. Well this one is pretty much your choice. You can buy it with Zen, or earn it in game, in a large variety of ways. It'd take way too long to go over every possible choice here.
Expertise is gained while leveling up, and normally used to train your BOFFs up in their skills. Once you hit level 50, it's easily gotten through doing almost anything.
Outpost Provisions, as mentioned, these are gotten from your replicator.
Data Samples/Particle Traces. Aside from buying them off the Exchange, you can farm them by scanning anomalies in various missions and star clusters, along with Duty Officer missions (usually under the science category). If you do the normal dilithium mining each day, that will also usually gain you particle traces. Some of the Astrometric Scientist DOFFs can give extra chances to gain more Particle Traces when you scan anomalies, which can help ease the trouble of getting those.
Commodities can be replicated, but I don't recommend it for large amounts due to the cost. Instead it's a very good idea to look at the various cheaper vendors that can be found throughout the game, both on the various hubs (like DS9) and galactic map. On top of this, the Tuffli Freighter and Suliban Cell Ship is extremely useful, because it has a Quartermaster who will always sell them for the lower prices. Plus, for Federation players only, if you have a Ferengi character, you will get a discount with the other cheaper prices.
Also, for any fleet who's unlocked tier 2 Embassy, there's a special upgrade which can unlock a commodity vendor at the Embassy who will sell some of the more expensive commodities for an excellent price. In fact with this vendor, you can get some of the most expensive commodities for the cheapest anywhere, even with a Ferengi buying them from somewhere else. (It is worth noting that with this special vendor, the Ferengi's do not get an extra discount)
Duty Officers. Past buying them off the Exchange, you can buy DOFFs out of your Starbase using Fleet Credits. Doing that is a good way to basically re-use your FCs for the sake of the fleet, and fill out projects. It's also a good idea to do your recruitment missions at the Academy (can be done at a high enough tier Starbase), to get extra DOFFs once in awhile.
There are also plenty of DOFF missions to get them outside of normal recruitment. Such as taking a higher level DOFF and de-grinding it into 3 lower level ones. A purple can turn into 27 white DOFFs if you so chose by doing this method. There's also various things such as doing exchanges, which is where you take one DOFF and turn it into another DOFF (Officer Exchange, Asylums, and others).
Doing Duty Officer missions can be quite useful in the long haul, because when you gain 110,000 exp in an area, you can go to your Starbase, and turn 10,000 of that exp into 75 fleet marks (100 on a critical success), guaranteed. Over time, if you DOFF heavily that can add up considerably, especially if you do even one turn in a day. Add in multiple people and/or multiple characters per person, and it will add up considerably. Theoretically, a person or group of people doing that enough could fill up fleet marks without ever doing anything else, if they did enough DOFFing.