The only real admiral problem that exists is that there isn't any new gameplay options that unlock at Admiral that set the rank apart from any other rank before it.

Here's how I would redo things:

Level 0 (Tutorial) - 4th year cadet.
Level 1-5 - Ensign
Level 6-10 Lieutenant Junior Grade
Level 11-20 Lieutenant
Level 21-30 Lieutenant Commander
Level 31-40 Commander
Level 41-50 Captain.

Cadet would be the tutorial, in which you command a space and ground mission like in the existing tutorial and when it is completed, you find yourself in one of the holodecks at Starfleet Academy, having just completed your final exam simulation. The subject matter of the tutorial would be Federation vs Klingon, because at the time of graduation, the KDF and UFP are at war.

Ensign and Lieutenant Junior Grade would have limited character gameplay to service on an NPC ship. The one which the player is on durring the Borg attack. The captain would be randomly generated based on the same sort of mechanics that control Bridge Officers, as would the senior staff of the crew. The ship would go to randomly generated missions similar to the ones we experience in the star cluster exploration missions. We'd be ground crew sent to deal with whatever circumstances arise. Upon reaching Lieutenant Junior Grade, we would start alternating between Tactical and Helm missions. At level 6, 3 new ensigns would come aboard, one of each division. At Level 10 the ship would be summoned to its encounter with the Borg and things play out as normal from there. You get to choose your first subordinate at this point, one of the three ensigns that joined the crew when you hit Level 6. Completing the Borg encounter and the death of your captain and most of the other crew, you get a field promotion to Lieutenant, and that ensign you chose for the mission gets promoted to Lieutenant Junior Grade, and will be assigned to you by Admiral Quinn.

At Lieutenant, the game begins as normal.

At Lieutenant Commander you begin being able use the DOff system.

At level 50, Captain, you are offered promotion to Commodore. (it is war time, after all). If you accept, you receive an office on Earth Space Dock, accessed as a linked door on ESD's lower level. At this stage, a Strategic Command game similar to the DOff system becomes available.

Player-run facilities would also be a priority if i were designing this. One such facility would be a shipyard, where player fleets may coordinate construction of a wide variety of vessels. These would factor into strategic command gameplay.

Strategic Command involves the requisitioning of Starships and the assignment of Bridge Officers to their key positions, promoting a Commander-ranked Bridge Officer to Captain and sending the ship to different places where depending on what skills and abilities you slotted into that ship, or a squadron of ships, different outcomes that have a tangible effect can occur. It is only through Strategic Command assignments that Bridge Officers can be killed and ships may be lost.

When a Boff is killed, he's gone forever. When a SC ship is destroyed, it's destroyed forever.

Actually, the access to Commodore comes at Level 50 and an investment of 243,000 RD.

After accumulating enough Merrit as Commodore, and if you have 437,400 RD, you can advance to Rear Admiral (no more lower or upper half. Commodore replaces Rear Admiral lower half)

After accumulating merrit as Rear Admiral, and if you have 787,320 RD, you become Vice Admiral.

After accumulating merrit as Vice Admiral, and with the investment of 1,417,176 RD, you reach Admiral.

Fleet Admiral would remain unattainable to players. There always should be mission-givers who outrank every player.

Regarding merrit, it is gained by having Strategic Command assignments completed successfully. And it would be lost if they fail. Lose enough merrit and you will be reduced in rank and will have to make the RD investment again to get promoted again.

The higher in Strategic Command you get, the greater the cost of shipbuilding and crew assignments... For example, at Commodore, the SC ships may be crewed by common Bridge Officers and equipped with common gear. However, at Rear Admiral, all crew and gear must be uncommon. At Vice Admiral, it would be Rare. and at Admiral, it would be very rare. So the the higher into the Admiralty you go, the greater the risk each mission would have, as well as the greater consequences for success or failure.

Using Purple gear or crew for anything other than Admiral-level SC assignment would only put those resources at risk. They do not affect the potential for success.

Bridge Officers obtainable only through one-time limited means cannot be used in SC assignments.

That is what I would do for an admiralty metagame