normally that would be true but then also there isnt any "AA" weapons and even proper anti air weapons can not get the job done in real life with a small fighter and if a battle ship has anti air weapons then why cant a small ship have ship buster weapons?

no your all wrong
the reason the damage is higher on the battleship than the frigrate
is because there is more area that can take damage
making it cost more to repair
and the deck space can take more damage and its easyier to kill some huge heavilly armed ship with some
nice coodinated strikes
because there is more area to take damage rather than this small extremely hard to hit ship
meaning that your deck is a weakness
evens out usefullness

The real reason the the big ship can take more damage is because Dan decided that's what he wants. He decided that he wanted people to be able to spend their rank points on decks or crew or cargo space. He wants people to be able to do what they want in the game and play to a style that suits them otherwise every rank up would just make your ship bigger and tougher.

Have any of you considered that maybe, your manoeuvrability would suck at a higher level. Put a jet engine on an F-16, go do some loop the loops and (im sorry) DO A BARREL ROLL. Then put 2 of those engines on a 747. It will fly, but not well, due to its large size it has less manoeuvrability. What might makes sense is that ships could have a passive increase in hull at each level.

Assuming same everything:
The bigger ship moves slower and have a bigger area, so it will be hit for more dmg. This is the current system and is fine.
When you say bigger ship can take more punishment, you are ASSUMING that it have THICKER armor(HP) and/or same thickness of armor but bigger area of it.
Well, what if the HP(armor) in game is a SET amount of SAME sized plate, that is it gives a SET VOLUME of armor each? That would mean that while having same total VOLUME for the same HP, the bigger ship have a THINNER plating, and thus, given same HP, easier to kill.

Bigger ship can take more punishment when it have the same THICKNESS of armor, with that said, it will require more VOLUME of armor and hence more total HP. It have the deck area to equip the additional hull modules to achieve that, why doesn't it?

So, your "in real life" example doesn't hold water, and in-game mechanic is dan's one man empire. So the case now falls in a hole~

What you are forgetting though is that damage is not determined by the amount of platings you have but by a ship's DEFENSE (which in this case, is actually composed of thrusters and dampeners). What that means is that a smaller ship actually also needs less defense (or thrust) in order to move. They move quicker than the heavier ships, which is why they take less damage because they are harder to hit (not just because they are smaller, but also because they are quicker).

Think back to Star Wars: A New Hope. They took on a freaking Death Star in X-Wings, but it worked because the X-Wings were small and agile. They could move quicker than what they could be hit. The Empire had to send out Tie Fighters to take them on. It's not becase they were going to make quick work of it, it's because the Death Stars OWN defenses were not up to the task of taking down quick, small and agile fighters. Its own defenses were too slow.

It's the same difference between a frigate and a battle ship in this game. Yes, the battle ship has bigger guns, but that's the point. Its guns are designed to take on other BIG ships. Against small ships, these weapons become useless because they cannot move quick enough to take out the smaller, faster ships.

Now, if you're going to say that a massive ships has the highest end thrusters and dampeners and the smaller ships has low grade tech, remember, the smaller ship requires less energy to go faster. It has less weight to pull, unlike the larger ships.

you're all forgetting that galaxy legion takes place in a separate universe. therefore physics here doesnt necesscerily apply there. dan, god of that universe, rewrote physics there so that little ships take less damage. and thats the end of the story. no logic is necessary