Actually , i can't make all of your suggestion every guy has a game style and its hard really hard to find the one that i need. i'm gonna research high enough the railguns (For RP reasons and because  i love kinetic weapons ^^)

there is a check mark for keep excess crew capacity in the top right, from there crew modules can be added.

Also why the cryo births? those are meant for picking up escape pods. better suited for a dedicated and disposable hospital ship

Unfortunately it has some killer flaws.  The biggest are that it lacks flight crew berths for the fighters, and it has no active sensor to spot enemies. Less important, but still very serious is that it only has enough magazine space for about 250 size 5 missiles. 250 missiles will go really, really fast between 30 standard launchers and bombers.  Of lesser concern would be the high number of fire controls - you probably won't ever need 15 fire controls for 30 launchers. I recommend 5 or 6 at most. 

I estimate at least 15,000 tons of your ship is devoted to armor, which is nice if you're being pounded with warheads but once you shoot your bolt you're defenseless against a single FAC with an energy weapon.

I would suggest going down to 15 armor layers, removing 10 of your fire controls, and using the tonnage gained on an active sensor (preferably 2 for redundancy on such a large warship) and magazines.

Your escort frigates also need active sensors for spotting missiles.

AM Frigate :
that was a fail x)
Frigate Leader:
You actually see everything and how i think oO i'm gonna try to fix that
LM Frigate :
5000t of engine 2x50HSengine (1 = 1500 EP) , MFC , Missile launcher , ECCM , Magazines : 2625t , 2 fuel Storage - Very large : 2000t , what left is for engineering spaces , damage control crew quarters etc....
EDIT : here is the fixed versions :

Achilles Mk-2.5 class AM Frigate    15 000 tons     447 Crew     7746.2 BP      TCS 300  TH 3000  EM 0
10000 km/s     Armour 10-54     Shields 0-0     Sensors 1/1/0/0     Damage Control Rating 45     PPV 15.4
Maint Life 7.1 Years     MSP 8230    AFR 70%    IFR 1%    1YR 286    5YR 4290    Max Repair 750 MSP
Intended Deployment Time: 16 months    Spare Berths 1   

ME 1500 EP Internal Fusion Drive (2)    Power 1500    Fuel Use 55.11%    Signature 1500    Exp 15%
Fuel Capacity 2 700 000 Litres    Range 58.8 billion km   (68 days at full power)

Single MW Mk-2.5 Gauss Cannon R5-17 Turret (11x5)    Range 50 000km     TS: 32000 km/s     Power 0-0     RM 5    ROF 5        1 1 1 1 1 0 0 0 0 0
AMF Mk-2.5 Fire Control S03 60-32000 H50 (11)    Max Range: 120 000 km   TS: 32000 km/s     92 83 75 67 58 50 42 33 25 17

This design is classed as a Military Vessel for maintenance purposes

I don't know why but the range after i add it of  the Fire controls UP without reason... i actually verified it has the good range when i created it
I was wrong all the time it was the "50% Accuracy at Range: 60 000 km" --'

Apache Mk-2.5 class Frigate Leader    15 000 tons     413 Crew     3699.2 BP      TCS 300  TH 3000  EM 0
10000 km/s    JR 5-100     Armour 8-54     Shields 0-0     Sensors 280/1/0/0     Damage Control Rating 35     PPV 0
Maint Life 2.69 Years     MSP 2389    AFR 116%    IFR 1.6%    1YR 472    5YR 7084    Max Repair 750 MSP
Intended Deployment Time: 16 months    Spare Berths 3   

FL J15200(5-100) Military Jump Drive     Max Ship Size 15200 tons    Distance 100k km     Squadron Size 5
ME 1500 EP Internal Fusion Drive (2)    Power 1500    Fuel Use 55.11%    Signature 1500    Exp 15%
Fuel Capacity 1 900 000 Litres    Range 41.4 billion km   (47 days at full power)

LMF Mk-2 Active Search Sensor MR205-R100 (50%) (1)     GPS 14700     Range 205.8m km    Resolution 100
AMF Mk-2 Active Search Sensor MR29-R1 (50%) (1)     GPS 210     Range 29.4m km    MCR 3.2m km    Resolution 1
F Thermal Sensor TH20-280 (70%) (1)     Sensitivity 280     Detect Sig Strength 1000:  280m km

This design is classed as a Military Vessel for maintenance purposes


Here is the new designs :

Achilles Mk-2.5 class AM Frigate    15 000 tons     491 Crew     10505.2 BP      TCS 300  TH 3000  EM 0
10000 km/s     Armour 10-54     Shields 0-0     Sensors 1/1/0/0     Damage Control Rating 45     PPV 11
Maint Life 7.31 Years     MSP 11161    AFR 70%    IFR 1%    1YR 366    5YR 5493    Max Repair 750 MSP
Intended Deployment Time: 16 months    Spare Berths 1   

ME 1500 EP Internal Fusion Drive (2)    Power 1500    Fuel Use 55.11%    Signature 1500    Exp 15%
Fuel Capacity 2 250 000 Litres    Range 49.0 billion km   (56 days at full power)

MW Mk-2.5 Gauss Cannon R5-17 (11x5)    Range 50 000km     TS: 10000 km/s     Accuracy Modifier 17%     RM 5    ROF 5        1 1 1 1 1 0 0 0 0 0
AMF Mk-2.5 Fire Control S04 96-32000 H50 (11)    Max Range: 192 000 km   TS: 32000 km/s     95 90 84 79 74 69 64 58 53 48

This design is classed as a Military Vessel for maintenance purposes

Apache Mk-2.5 class Frigate Leader    15 000 tons     413 Crew     3629.2 BP      TCS 300  TH 3000  EM 0
10000 km/s    JR 5-100     Armour 8-54     Shields 0-0     Sensors 280/1/0/0     Damage Control Rating 35     PPV 0
Maint Life 2.56 Years     MSP 2344    AFR 116%    IFR 1.6%    1YR 500    5YR 7497    Max Repair 750 MSP
Intended Deployment Time: 12 months    Spare Berths 1   

FL J15200(5-100) Military Jump Drive     Max Ship Size 15200 tons    Distance 100k km     Squadron Size 5
ME 1500 EP Internal Fusion Drive (2)    Power 1500    Fuel Use 55.11%    Signature 1500    Exp 15%
Fuel Capacity 2 000 000 Litres    Range 43.5 billion km   (50 days at full power)

LMF Mk-2 Active Search Sensor MR205-R100 (50%) (1)     GPS 14700     Range 205.8m km    Resolution 100
AMF Mk-2 Active Search Sensor MR29-R1 (50%) (1)     GPS 210     Range 29.4m km    MCR 3.2m km    Resolution 1
F Thermal Sensor TH20-280 (70%) (1)     Sensitivity 280     Detect Sig Strength 1000:  280m km

This design is classed as a Military Vessel for maintenance purposes

Pegasus Mk-2.5 class LM Frigate    15 000 tons     340 Crew     3468.2 BP      TCS 300  TH 3000  EM 0
10000 km/s     Armour 10-54     Shields 0-0     Sensors 1/1/0/0     Damage Control Rating 41     PPV 16.5
Maint Life 4.32 Years     MSP 3035    AFR 85%    IFR 1.2%    1YR 262    5YR 3931    Max Repair 750 MSP
Intended Deployment Time: 16 months    Spare Berths 1   
Magazine 802   

ME 1500 EP Internal Fusion Drive (2)    Power 1500    Fuel Use 55.11%    Signature 1500    Exp 15%
Fuel Capacity 2 000 000 Litres    Range 43.5 billion km   (50 days at full power)

LM Mk-2.5 Size 5 Missile Launcher (33% Reduction) (10)    Missile Size 5    Rate of Fire 430
LMF Mk-2.5 Missile Fire Control FC117-R100 (50%) (10)     Range 117.6m km    Resolution 100
Size 4.92 Anti-ship Missile Cobra Mk-2.5 (160)  Speed: 32 500 km/s   End: 54.8m    Range: 106.9m km   WH: 10    Size: 4.92    TH: 390/234/117

ECCM-3 (2)         Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s

This design is classed as a Military Vessel for maintenance purposes

for the missile , i'm gonna upgrade it later

Look at it this way, you should be aiming for ~33% of the ship's tonnage as engine. For 15k tons, that is 5000 tons of engine (2 50HS engines). Not only are they more efficient, being bigger, but you can scale down the power modifier to increase efficiency more without impacting speed as much. And what I meant for reduced size launchers is scaling the launcher size, not the missile size. You see the box with the 25% reduction, 33% reduction, etc? That is what I mean. Sure they may fire slower, but having a larger initial punch pays out quicker in engagements.

A spot where you seem to be bleeding tonnage is in Sensors and Fire Control. Missile engagement should be around 50m km to 100m km. When you adjust missiles in the future to be around that range, you can see better effectiveness in the missiles and more space saved by matching the sensors and fire control to that range. Also, taking another look, the Apache has way too large of passive sensors. Reduce their size by half or simply remove one of them.

As posted above your designs have way too small an actual mission package. 
Unless for some reason they need to operate ridiculously far out, there is really no reason why the range, but more importantly maintenance life and deployment time need be so large.   I find it unlikely these ships will ever need to be on station for 3 years at a time and an 8 year maintenance life is pretty high.   You will probably be updating these ships before they even need overhaul.   If additional fuel and MSP are needed, they can always be placed on a fleet support. 

Additionally you have almost as much tonnage in fuel as in engines.   Rejigging to use more engines and tweaking your power ratios could give you the same range and speed for less tonnage i am sure. 

The missile launch frigate is the worst offender.   Firing 3 missiles at a time it is unlikely to penetrate missile defences.   

My advice would be to free up space on your leader and then mount your active sensors on that.   You can put a small backup on your other ships for redundancy.   Then use that space on your other ships to add more weapon systems.   I would recommend dropping your launchers down to using 50 or 25% size reduction to help pierce PD fire, however if the enemy has long range AMMs then this could be counter productive due to the reduced rate of sustained fire.   You should really be aiming for a lot more launchers though. 

I dont mean this as flame in any way, just trying to help you learn. 
-Graham

Edit- You said size 50 engine, are you implying you don't already have a size 50 engine? on a 15000t ship 2500t of engine is still pretty small.

I'm a bit confused where all your tonnage is going. The Pegasus is a 15,000 ton ship with 2500 tons of engine and maybe 1500 tons of armament (undergunned and underengined compared to most designs), 2600 tons of engineering spaces,and another 2000 tons of fuel.    At your tech level the thick armor shouldn't be prohibitive. Are you using size 1/10HTK magazines or something? 

For reference, a common 9000-ton  Precursor ship in my games mounts 7 size-4 launchers with deeper magazines.

Also, it may help you control maintenance costs if you make an engine without thermal signature reduction.  TH reduction is valuable in scout ships, but it balloons the costs of engines to insane levels - they become enormous maintenance hogs.