I use Thunderhorses as main transport. Deliverator used to be my space shuttle, but I have since switched to the Prospector.
Deliverator: Space for 10 crew or an HWP and 6.
Two exits, a single door and a 2-wide gate, both protected by doors. The 2-wide one is in the air.
Spaceworthy
Positives: Your crew inside is protected from grenades and shots by doors.
Enemies can use only the bottom entrance to infiltrate the vehicle.
Negatives: Small
If you take a non-flying HWP and it exits the vehicle, it can not retreat.
Prospector: Space for 12 crew or 8 crew and 1 HWP
1 2-wide exit, 2 1-wide exits, one of which is in the air. All covered by doors.
Spaceworthy
Positives: Your crew inside is protected from grenades and shots by doors.
EDIT: 4 free chunks of Metal ore per mission
Negatives: Large dead angle on small door due to inaccesible tiles.
Thunderhorse: Space for 24 crew or 4 HWPs and 8 crew
2 2-wide ramps to the ground.
1 2-wide ramp to the roof
1 1-wide ramp to the ground, protected by door.
Positives: Large
Roof access, allowing HWP to deploy in spite of possible obstructions and non-flying Snipers/Archers to deploy to a semi-safe location.
Negatives: The item pile can be hit by a stray grenade.
No doors on the large ramps, allowing hostiles to shoot inside.