So, I am debating pairing the typical Whisper (VI, FCS, Agent Kallus and Adv. Cloak) and Wampa with the Upsilon Shuttle. I am just debating what upgrades/pilot to put on the Shuttle to make the combo most effective.......................

If you are wanting to use Palpatine, I think that Kylo would be his ride of choice in that squad. Kylo's ability adds a little bit of a disincentive to the strategy of "kill the shuttle first".

"Wampa" (14)

"Whisper" (32)
Veteran Instincts (1)
Fire-Control System (2)
Agent Kallus (2)
Advanced Cloaking Device (4)

Kylo Ren (34)
Adaptability (0)
Fire-Control System (2)
Emperor Palpatine (8)

Total: 99

This uses Dormitz in a support role. Operations Specialist will ensure that Whisper gets a focus token whether his attack hits or misses. Dormitz can hand off a target lock when he pulls a green. This allows Whisper to change targets more easily or increases the chances for Wampa to trigger his ability. When Wampa's ability gets used it will trigger Operations Specialist giving Dormitz a focus token to use when attacking. Dormitz will use coordinate so that one of the other ships can take an evade or repositioning action in addition to the focus action. Advanced Sensors frees Dormiz up to bump or pull red maneuvers while still being able to use Coordinate.

Ion Projector and the shuttle title add a little bit of control and potentially makes it dicey to try and knife fight around the shuttle. Ion Projector could be swapped out for Anti-Pursuit Lasers if you prefer the damage potential over ionization.

Whisper has a 2 point initiative bid. Switching FCS out for Sensor Jammer will make Whisper a bit more durable. Systems Officer Dormitz can help shore up the loss of FCS a bit if you go this route.

"Wampa" (14)

"Whisper" (32)
Veteran Instincts (1)
Fire-Control System (2)
Agent Kallus (2)
Advanced Cloaking Device (4)

Lieutenant Dormitz (31)
Advanced Sensors (3)
Systems Officer (2)
Operations Specialist (3)
Ion Projector (2)
Kylo Ren's Shuttle (2)

Total: 98

The more that I think about it, the more I like the way that Wampa combos with Dormitz with Operations Specialist and Systems Officer on Dormitz. The Target Lock from Systems Officer gives Wampa a reasonable chance to reroll his two dice attack into a crit. If he gets his crit and uses his ability then Operations Specialist will generate a token. If his two dice attack doesn't end up with a crit and misses like they are wont to do it still generates a token. Dormitz's ability gives his squad mates a long leash.

Striden hux systems off could be nice for both offense and buffering whisp by letting her evade without sacrificing offensive focus

Rerolls are nice for wampand also lets him evadw

Condition on shuttle