My experience with DA ships has been almost the exact opposite of yours; I've always found Vapors to be very survivable, and the Fractus to hang back far enough to stay out of trouble. Vapors are fast, have an omni shield, and have a ship system that's basically a get-out-of-jail free card that the AI is very willing to use.
Since our experiences are very different, this sounds like a loadout issue to me; can you post pictures of your Vapor and Fractus loadouts? Vapors really want the range of medium ballistics and don't have the flux to use many energy weapons at all, so if you're sticking 2x pulse laser on your Vapors they're probably soft-fluxing themselves to death. The Fractus has a universal slot that really should be a missile slot, because it doesn't have the flux to mount 3 smalls and a medium.
I try to keep my weapon flux stats as close to the vent rate as possible. Pulse Lasers are for Cruisers and up, IMO. Even Destroyers have trouble balancing the flux of Pulse Lasers. Frigates certainly wouldn't be able to handle the flux rate of a Pulse Laser unless that was the only weapon it had and nothing else.
The Fractus: 1 Recson V, 3x IBIS. Hull Mods: Insulated Engine Assembly, Expanded Deck Crew
The Vapors: 1 Glowtusk Linear Rifle, 1 Grave HMC, 2x IBIS. Hull Mods: Insulated Engine Assembly
My personal Vapor has 2x Magicbox PD instead of the 2x IBIS but everything else is the same.
Weapon groups on the Vapors are set to have the Glowtusk to autofire while the Grave HMC is manually controlled. I know the AI kinda doesn't care and will tend to fire HE weapons at shields anyway.
The Insulated Engine Assembly is on every ship in my fleet. Its there because I'm currently trying to go all privateer against Hegemony and Tri-Tachyon merchant fleets to generate income. So I'm going all sneaky ninja like with my transponder off and going dark a lot to avoid patrols. I want the smallest sensor profile I can get ATM. Insulated Engine Assembly doesn't technically have to be there and I don't intend for it to be there permanently, but it only costs three OP on frigates. Once I'm done raiding merchants I was going to dump Insulated Engine Assembly anyway.
Question, are there any other mods in play?
It might be that you are using some fairly broken mod and the enemy is using weapons from that mod do they end up stronger than they should.
For this play through I have these mods enabled.
Nexerelin
Dynasector
Combat Chatter
Common Radar
LazyLib
Omnifactory
Portrait Pack
Practice Targets
Ship/Weapon Pack
Unknown Skies
Upgraded Rotary Weapons
Audio Plus
GraphicsLib
Lightshow
Blackrock Drive Yards
Shadowyards
Underworld
Diable Avionics
SCY Nation