1) If people want to make Transports generally tougher - let them use Gunboat equipment, but limit them by their powercores.
This way you will see transports using less of the power-hungry Mortars and Missiles - and more of the standard faction guns. This is a better situation than making up a slew of new weapons and equipment for them.
2) /group formation bonus? Let it be a bonus to powercore regen perhaps? Let it only apply to transports in formation. This allows transports to stay in turret mode and put up a wall of fire - whilst having less worries about running out of firepower.
3) What about sole traders? Let them take up smuggling as a hobby! Give Freighters a Cruise Speed boost (combined with Dusty's Mission Cargo Concept smugglers would be well sorted).
4) Increase profits? Remember - whatever happens with the economy, people will always flock to the best and easiest way to make money.
If there is to be a route bonus - then let it rotate among the trading factions every week - we have a lovely updater that can do that for us!
Otherwise - one or two lucky runs will get all the attention - and the rest will be a waste of time!