Smart Han/Poe/Corran and TLT spam are my main concerns.

99pts

"Whisper"

Decoy

Fire-Control System

Flight Instructor

Advanced Cloaking Device

"Zeta Ace"

Push the Limit

Darth Vader

Veteran Instincts

Proton Rockets

Advanced Targeting Computer

TIE/x1

In my mind:

Zeta blocks

Whisper shoots first

Vader unloads Prockets

If those specific ships are your concern, i would go with Sensor Jammer. The only ship that can nullify its use consistently is Poe (although blocking with Zeta solves that problem too). Drop Flight instructor for it (Flight Instructor is not really good on Whisper neither---her free focus means she won't even be using it against higher PS, and spending 4 points to re-roll 1 blank green die vs PS 2 is a bit meh).

Edit: alternatively, drop Whisper in favour of Echo who might benefit more from the Vader/Decoy combo (although you have to be a bit more careful about keeping them within range 2 of each other). At least Echo benefits a bit more from Flight Instructor regardless of enemy PS when getting shot at.

FCS is mandatory for me as it guarantees lethal R1 5 hits attacks so not ready to give it up.

Flight Instructor can be helpful against high PS Gunner and a life saver against swarms or bbbbz. If it works once it costs like a Shield Upgrade and there are not many damage mitigation crew for imps.

Echo recon on the other side gives 4 points left for EU on Vader...

Thanks for your inputs!

Decoy is only good on Echo (with another PS9 pilot in squad).

On Whisper, just get veteran instincts for PS9 - one point cheaper and you don't have to be in range.

This way, you have one extra point to replace Flight Instructor (not so useful on Whisper with her extra focus) with Gunner, which just owns everything with FCS.

If you want to build a super-defensive whisper, then I'd suggest sensor jammers + rec spec + veteran instincts + ACD, it can stand up to TLT barrages and can usually mess up the gunner ability on PWTs