As many people know that when you get to Commander, you currently only get 80,000 Dilithium for a ship when the amount needed is 100,000.
As a result, it's currently very difficult to get a commander level ship.
The easiest way to handle this is to simply not buy a Tier 2 ship and grind through LT commander in the light cruiser. But if this is not your cup of tea, it is possible to build a Tier two Connie to handle the commander level missions.
As such I am putting out this guide for a Tier two commander level cruiser.
The real thing is ship Bridge officer powers.
Ensign power Science team 1
Beam overload 1
Emergency power to shields 1, Reverse Shield Polarity 1
Emergancy power to weapons 1 or Engineering team 1.
For weapons and gear, I suggest Buying with your dilithium one shield array.
[Resilient Shield Array Mk VI [Cap]x2]
Then when you run the mission Past Imperfect and choose,
[Efficient Impulse Engines Mk IV] as I run with these engines up to Rear admiral and beyond.
As for ship weapons Run the missions Doomsday Machine twice to get two
[Hargh'peng Torpedo Launcher Mark VI]
and the Devidian mission Everything old is New and get two
[Phaser Beam Array Mk VI [Dmg]x2]
The basic strategy around this is that you run in attack mode as much as you can, changing to defense as needed when facing battle ships, and such. Also When the space combat gets too... hard switch to a defensive ship setting with your shields to 100.