I created some additions and modifications to your rules - what do you think?

Non-Standard Starmada Special Rule: Ship Power and Command Crew
In the Star Trek universe, managing your ship's crew, officers, systems and power has always been an important part of the lore - how often have you heard “All power to shields!” or “Power to impulse engines!  Evasive maneuvers!” or “Direct all efforts to damage control!” in an episode? 

When playing in the Call to Arms universe, each ship gets an additional basic rating - like their CRAT - derived from the ship's characteristics. This rating represents the talent pool of the ship's crew, the sophistication of their engineering and power sources, and their capacity for cinematic derring-do in the face of danger.

How Much Power Does A Ship Have?
A ship has the following amount of “Power and Command Flexibility”:

Power = Square Root of ((Hull * Hull * Thrust) * .05)

Round all decimals up or down to the nearest whole number.  Exact .5 decimals should be rounded up rather than down.  Examples:

A Federation Galaxy class battleship has Power = SqRt((17 * 17 *3)*.05), or 6.58 = 7 power.
A Cardassian Galor class standard cruiser has Power = SqRt((13*13*4)*.05) or 5.81 = 6 power.
A Romulan Griffon class light cruiser has Power = SqRt((9*9*5)*.05) or 4.5 = 5 power.
A Federation Nova class survey ship has Power = SqRt((6*6*7)*.05) or 3.57 = 4 power.
A Klingon B'Rel class attack corvette has Power = SqRt((5*5*6)*.05) or 2.73 = 3 power.

Losing and Recharging Power
Ships may use power in a variety of ways during the turn.  When they do so, they ‘mark off' a power box with a U.  Whenever a ship is activated to move, it rolls a dice for each ‘marked off' power box with a U.  On a 4+, that power box is ‘recharged' for the turn.  If a power box fails to recharge, mark it with an ‘R'.  A power box marked with an ‘R' is automatically returned to full strength when the ship is selected to move in the move phase.

Power is treated as ‘Munitions' during the damage phase.  If a ship becomes damaged, it marks off ⅓ of its power boxes with a D.  If it becomes disabled, it marks off the next ⅓ with a D.  Power boxes with a D can never be recharged when a ship is selected to move.  Ship power is not protected by Reinforced Systems and always is lost at the rate of ⅓ per damage level.

Using Power

Initiative Phase

‘Power to Sensors!' - A ship may boost its Sensor (Standard Starmada: ECM) rating by 1 for each point of Power spent.  This may then be used as normal for either ECM or EPM before the end of the initiative phase.  These additional levels of Sensors do not count for the purposes of marking off Sensor damage boxes and disappear at the end of the current turn.

‘Power to Shields!' - A ship may boost its Shield Strength (Standard Starmada: Armor) rating by 1 point for each point of power spent.  All Shield Strength boxes are added ‘in front of' the current Shield Strength boxes and are lost first if the ship takes damage.  Shield Strength cannot be added above the maximum Shield Strength of the ship, total. The temporary Shield Strength boxes provided by this use of power disappear at the end of the turn in which they are created.

Movement Phase

‘Power to impulse engines!' - A ship may boost its Thrust rating by one point for each two points of energy spent.  These temporary points do not count for the purposes of marking off Impulse damage and are marked off at the end of the current turn.  Temporary thrust points may be used to commit Evasive Maneuvers as per the Starmada rules.

‘Power to tachyon emitters!' - The only known way to pierce cloaking devices is the careful use of tachyon emitters.  A player may spend one power point to force one enemy ship to re-roll the ‘detect cloak' dice when that ship is selected, or roll an additional time if the ship was already selected to move this phase.  If a ‘1' is rolled, the opposing player must stop re-rolling.   

Combat Phase
‘Power to targeting sensors!' - A ship may spend two Power points to ignore any -1 penalty for one weapons battery.  Ex: A ship may spend four points to ignore a -2 penalty imposed on one of weapon battery, or two ignore two -1 penalties imposed on two separate weapons batteries.  A ship may NOT spend points to ignore the penalties imposed by damaged weapons batteries.

‘Power to weapons!' - While not all weapons are responsive to additional power input, most starships mount energy weapons which can take an overload charge.  For every two energy points spent, any weapon with no special qualities (other than ‘Diffuse') may move the final result of its number of attack dice up by one. .  This does not modify and is applied only after the +/- on the standard Starmada chart, but the TOTAL number of attack dice the ship may roll.  For example, if a Mk 9 Phaser Emitter (Rng 9 / Diffuse) whose final attack dice number was 1 spent four energy points, it could roll 3 attack dice.  This can be used to move a ship up from zero attack dice.

‘Power to structural integrity!' - If a ship elects to engage in Damage Control rather than firing, the ship may spend up to two points of energy on each Damage Control dice roll.  Each point of energy adds +2 to the Damage Control dice.  Thus, if one point of energy is spend, a dice roll of 3 counts as a 5.  If two are spent, it would count as a 6.  The player may choose which dice to spend energy on, but must choose before the dice are rolled.