You can argue that character skillsheets are all about tradeoffs and having varied playstyle, choices and power variables, and that's great when it's fun, but being weaker or cutting out flying entirely and missing that whole amazing gameplay experience is a bad outcome, very bad.
This comes up every so often. I think your observations are pretty much spot-on, but not the conclusions. The fleet skill points and personal flagship skill points are mixed in together in the same skill point pool so that the player has maximum flexibility in deciding where to allocate those points. If the player likes playing the game more like an arcade, then more points go into flagship skills. If the player likes playing the game more like an admiral, then more points go into fleet skills. This also changes throughout a playthrough; initially, I tend to take more flagship skills, but as my fleet gets bigger, I'll respec into more fleet skills, even though I'll generally always have between 4 and 7 points into flagship skills.
The whole point is that you can choose to go along many different paths, but you can only choose one at a time (or, technically, you can get up to 3 capstones, so that'd be up to 3 at a time). You can choose to be a fighter, or a cleric, or a mage, or a rogue, and play the game through that way, but you can't be a fighter/cleric/mage/rogue/artificer/bard/ranger/etc. all at once, which would make the player too overpowered and the game too easy. Each path needs to have something good, but also make you give up something good as well, so you can't do it all at any given time. That's how a lot of game balance works. If this game allowed you to do everything, i.e. say give you 40 skill points instead of 15, then a lot of the skills would have to be severely nerfed so that the game doesn't become too easy.
For a sufficiently skilled player, the flagship can generally do around 2x to 3x as much as the AI in that same ship. So the player's flagship is the single most influential ship in your fleet. That's why it may make more sense to put points into flagship skills rather than fleet skills.
It looks like your fleet is specializing in Best of the Best, Support Doctrine, and Hull Restoration. SD and HR are solid picks for the early game, but as you acquire and level up more officers, SD becomes less useful, and as your fleet gets more powerful and have less deaths, HR also becomes less useful. At that point it'll be worth respec'ing away from those skills and put your points elsewhere, such as flagship skills or other fleet skills, which will give you more points to put into the stuff you want.