Frankly there isn't much differentiation between the transports. Sure the agile one has a bit less HP... but frankly the cloaked transport is far and away the winner almost the entire time because it avoids getting shot to pieces by AI forces the overwhelming majority of the time. We could probably do with a couple additional transport types and then on top of that change the maximum fleet lines allowed by transport type. Such that transports with exceedingly high utility like the cloaked one aren't also going to be packing an entire forty line fleet around. This would also makes eyes more relevant again because other than death balling it with a topped off standard transport you'd probably have to approach it a little more tactically or actually hack it again for a change.
So the standard transport, absolutely no advantages at current over the others really. I'd suggest letting it keep the biggest allotment of ship lines. After all its just a great big transport with nothing special. May as well lets its advantage being the ability to have the most ships possible.
Agile is fast and pays for it in HP at current. I'd say reduce the HP penalty a bit and make it more a matter of it only gets 2/3 the ship lines of the standard transport. Still quite a bit, but its getting that extra speed by not being able to hold as much.
Cloaked pure and simple should get smacked with a significant maximum ship line capacity penalty. Outside of some tachyon detectors at the wormholes themselves or a couple sentinels with long range coverage it simply isn't at risk of getting hit. It should be a utility asset and not the primary flagship of the death ball of doom. Frankly the number of ships spawning from a fully stuffed 30+ line cloaked transport alone should be cluing the AI into where your ship is and getting it smacked. As a tactical asset it would still be stupidly effective at hacking things before your main fleet goes in. Or at raiding specific targets and then getting out.
As for additional transport types? Armored Transport, half the usual fleet line capacity but higher than usual defenses and takes reduced damage from things beyond a certain range. Great for kicking in the door and not getting rapidly shot to pieces by a mass driver on the other side of the gravity well if you didn't have a cloaked transport handy to hack it or raid it beforehand. And then the Escort Carrier Transport, again reduced fleet line capacity but comes with a built in allotment of drones that upgrade when it is upgraded. Additionally all ships being held within can be repaired at a certain rate unlike standard transports that don't repair ships at all while they are being carried. Functionally a great way to keep a fleet of frigates topped off as you move them to where you need them while the drones provide chaff so the more expensive frigates are less targeted.
