Ok, i try to answer every request
I have problems, installing the mod (sth. like NSIS Error: file corrupted, tried to dl it 5 times), so i donīt know if a suggestion is allready in the mod
If you have tried it 5 times with the same result try to change your download behavior like using or don't using a download manager / other download manager / alternate download mirror.
- Moveable Intrepid Nacelles (Using the Galaxy Integration Special Weapon), e.g. to make it run away fast in danger. Would make it a excellent vanguard.
The Intrepid already has the Tricobald Torpedo feature, making it also faster would affect balancing negative.
- Repair Authonomy: Makes Ships return automatically to Shipyard, if they exceed a specified amound of Damage (e.g. 75/50/20 percent)
First thing, i don't know if possible, but that also would be not a good idea that singe ships seperate from your fleet and move back to their shipyard by flying through the enemy base. it would also destroy the team management, you would also have to unselect every ship that leaves your fleet for repair. fleetops is not intended as a big-fleet-low-mangement mod.
- make superweapons only one a time buildable, without affecting Credits for other Ships (Another, but invisible Credit-Resource should do it), also try to limit starbase amount.
'Superweapons' is one thing we want to avoid with fleetops, we only have good big weapons you can build only a limited amount using the credits system
- Advanced planetary upgrades: Dont know, if it is part of FO, but colonizing Planets is the best thing of A2. The bad thing about it was that it was not consequently built into the game. There should be not only a planetary shield upgrade, but also a planetary defense. To power them up, they can only be built if a power plant is on the planet. But before that, you have to build settlements and farms to get more crewmen and increase "bithrate".
Planets come with beta 2. It is not sure yet if they will are for colonizing or just decoration. I like your idea, but that is simply not possible with armada.
- Bring back the Latinum. But only to be gained by trading. Because traiding is a key feature of an RTS. And the Fereghi have to do their part, too.
I would suggest to make traffic between starbase and trading station possible, because it is less like trading with yourself. Latinum could be useful to change Dilithium with Tritanium and event buing Ships from a Non Player Species.
I think Tritanium is good alternative to Latinum. We wanted to avoid the too game bothering resource management from original armada 2.
- Artillery, Assault Teams, Mines, Impulse Boost and other general special weapons should be used by nearly every playable species, but in different tech levels. That means one race has it early than the other one, which has other advantages.
Not every race has Artillery and of cource it is more or less different to reach the technologies. (ex. federation steamrunner - costs credits - romulan artillery - build regular)
- Special Weapons: Deflector Pulse, AMines for Defiant (very late to research), EMH, Peregrine Raider launching Norway Class (because of very big Shuttlebay), Sensor Probe... Please donīt make any Ship withoout a Special Weapon
Yep, out plan is to make every ship with a special ability, more or less important, active or passive.
- I hope the strength of the ships (shields, hull) are somehow fitting to their size, like in A1. That means a Akira is 65% of a Souvereign.
Yep, they do, i don't know if exactly 65%, but exactly this what balancing allows
- This Ships, I want to see in the mod: At least one-time seperateable Prometheus, Nova, Achilles, Norway, Peregrine, Runabout, Valdores, ...
And i hope you have thown out that ugly Ship Classes from Armada 2 (Iwo Jima, New Klingon Ships, New Borg Ships)
All ships have new models.
We cannot include every of the half million federation designs floating in the internet, just what balancing allows

A romulan Valdore will be in the game with the next beta.
Donīt forget the Cardassians* and Breen as playable Races in FO. They play very important roles in ST. Donīt say, they are part of the upcomming Dominion
race. The Federation, Klingons and Romulans are seperated, too.
*Of Course Cardis should have gullgrey/red bases and brightbrown/red ships.
The problem is that in armada 2 is a 8 race limitation, by that there will be a dominion only dominion and no cheap mixup like an alliance. The cardassians and breen will available as non player race for maps, you can overtake their bases if you intent to (and if you can do

)
Delta Quadrant Alliance (Talaxian, Hirogen, Malon, Krenim, Kazon, Vidian, Voth, Vadvahr, ...)
TOS-Timeline Federation (Using Ships from ST:TMP to TNG (except Galaxy)
The Gorn would be nice
The next release will include some new non-player races for the maps. the final release will include even more. But wouldn't you think a delta quadrant alliance would be a bit unrealistic, think about it

(Kazon, Krenim, Hirogen, Malon...)
Good thoughts in it.
But why not first play it and then make suggestions?

DOCa Cola