@Pillat
I only have a minute, so apologies if the below is only an outline, or has grammatical mistakes.
1) crew level is based on captain level.
2) if you are low level, then your crew is low level, and it will be hard to win boardings. As you gain level, your crew gets stronger.
@Pieter Boelen is right the crew doesn't get experience, but they borrow your level so they still go up over time.
3) enemy captain level is based on ship tier and type. As a rough estimate, take 7 times the number of tiers below 8, add (10 if navy, 8 if pirate, 5 if regular, 3 if merchant), add (8 if swashbuckler, 4 if seadog), and you have around the number.
4) a tier 6 navy ship has around a level 24 captain on mariner. A tier 5 merchant ship is about the same.
5) all navy ships have guards as crew, which are fairly standardized across levels, ie consistently good from standardized military training, they get +150hp regardless of level, and get +10 to their level from what it otherwise would be,
6) this is mostly a nerf from previous versions, where guards got +5hp per level and got the +10 levels. If you do the math, with their +10 levels, the +10 levels their captian gets, and the highish tier of navy ships, +150hp usually is substantially lower than the old +5hp per level, and about the same on the smaller navy ships.
In sum, if you are level 10 and attack a tier 6 navy ship, adding the guard and navy captain bonuses, your crew is facing an enemy crew that is going to have about 3x their level and +150 base hp.
You mention you think it has gotten harder to board navy ships--that could be true, but the change would have happened before my time I started playing so I wouldn't know. The only thing changed recently is the 150 base hp they are getting close to what they would get if they got the old +5hp per level multiplied by their high level on the smaller ships. Navy crews should be a bit weaker than before on higher tier ships now, and be rather consistent in the challange they pose from standardized military training.
The only other recent change is they can equip armor, but they should also have weaker weapons on average to balance it from no min cap (armor tables getting better as potential weapon tier gap increases, so they both do less and take less damage), and it sounds like the HP was the problem anyway, so it probaly isn't that.
It sounds like the source of this might not lie in the crews themselves, but your currently low level, and how morale and crew size affects hp.
What I understand from your post: basically you would like to see the morale and relative crew size differences exert a stronger effect on boarding HP, so that even if you are still only level 10 or so and facing crews 3x your crew's level, you can still win with superior numbers.
I think what you want is the functions in LAi_boarding, in the program/ loc_ai folder. Search for where morale and difficulty level go into the big HP difference equation (it is hard to miss), and you can finetune it to achieve the effects you are looking for.
(generally swamped at work and may not be around to answer replies, could be days or weeks before I can pop my head in again, just saw this at top of recent posts and figured I could provide a starting point to understanding what is going on)