Summary:

The idea behind this mod is to be able to use all the tech and support you have at your disposal without affecting your S-Rank scoring at the end of the mission. Also I am trying to shift the importance of certain aspects during the final scoring. These are my reasons to do it:

• Time bonus is halved: In order to balance things out, now that you can finish certain missions very, very fast using all your tools.
• Reflex mode doesn't affect the PerfectStealthNoKill Bonus: I think is unfair to give you an ability and then penalize you for using it. As long as you don't get an alert, you can obtain the PerfectStealthNoKill bonus. However, if you want to get the NoReflex bonus, well... you must not use reflex mode!
• Bonus score for completing objectives are doubled: This encourage you to complete the objectives rather than skip them.
• Stealth related bonuses are doubled: No Enemy Combat Alerts: + 10,000 (2x), No Kills: + 10,000 (2x), Perfect Stealth, No Kills: 40,000 (2x), in order to encourage a stealthy approach.
• NoReflex & NoRetries bonuses are doubled: This give you more incentive to complete the mission as lean as possible.
• Prisioners rescued bonuses are doubled: I am using Infinite Heaven fulton settings, so it is not easy to rescue prisoners and encourages me to do it. I recommend you to do it too.
• Headshots & Tactical takedowns bonuses are reduced: To discourage the farming of those activities during long missions, also you will be doing more headshots with Reflex Mode not affecting the Perfect Stealth Bonus ;)
• Enemy Combat Alerts penalty is cuadrupled: Because that's the idea :)
  

NEW VERSION 0.3:

Allows to get perfectStealthNoKillBonus using Reflex mode.  

Disables rank penalties for:

• STEALTH
• FULTON_MISSILE
• PARASITE_CAMO
• HIGHGRADE_EQUIP
• SupportHelicopterAttack
• FireSupport
  

Keep penalties for:

• Chiken hat
• Mugen Bandana
  

To balance things out, the bonuses modifiers are tweaked (in bold what was changed from previous version)(x = vanilla value): 

Play Rating score modifiers

Accuracy: Vanilla
Effective Interrogations: + 150
Enemy Combat Alerts: - 20,000 (4x) (LOL)
Re-Discovered Combat Alerts: - 500
Headshots: + 1000 
Hits Take: - 1000 (10x)
Markings: + 30
Neutralizations: + 200
Prisoners Rescued: + 10,000
Tactical Takedowns: + 500 (0.5x)
Time: 1/2 Vanilla (0.5x)

Bonuses score modifiers

Mission Tasks: Varies
First Bonus Objective: + 10,000 (2x)
Second Bonus Objective: + 10,000 (2x)
No Enemy Combat Alerts: + 10,000 (2x)
No Kills: + 10,000 (2x)
No Reflex Mode: + 20,000 (2x)
No Retries: + 10,000 (2x)
Perfect Stealth, No Kills: + 40,000 (2x) (it doesn't matter if you use reflex)
No Traces: + 100,000

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Check the other mods I have done to make the game more interesting:

Lose Marking on Death

[SBWM]

PREVIOUS VERSION 0.2:

Play Rating score modifiers

Accuracy: Vanilla
Effective Interrogations: + 150
Enemy Combat Alerts: - 10,000 (2x)
Re-Discovered Combat Alerts: - 500
Headshots: + 100 (0.1x)
Hits Take: - 100
Markings: + 30
Neutralizations: + 200
Prisoners Rescued: + 10,000
Tactical Takedowns: + 500 (0.5x)
Time: 1/2 Vanilla (0.5x)

Bonuses score modifiers

Mission Tasks: Varies
First Bonus Objective: + 10,000 (2x)
Second Bonus Objective: + 10,000 (2x)
No Enemy Combat Alerts: + 10,000 (2x)
No Kills: + 10,000 (2x)
No Reflex Mode: + 20,000 (2x)
No Retries: + 10,000 (2x)
Perfect Stealth, No Kills: + 40,000 (2x) (it doesn't matter if you use reflex)
No Traces: + 100,000