This is an interesting conundrum  I have found in games vs the AI at least . That AT's as fast and long ranged as Bombers will tend to totally replace sea transports. Over the long haul they just get more guys there quicker. 

I've  extensively modified the Enhanced Unit set as well as creating new units for both the old EDEE and now EDCE (just getting back into playing) to suit my gameplay on large maps. The normal Enhanced Set is fine for small maps; as you've noted it can often be modified to address some things like the AirTransport movement.

When modifying units for the game consider the size and type of map.  For a map 100 x 100 - it will take a transport or satellite 50 turns from side to side/corner to corner on a no wrap map. On a 400 x 400 map, it would take 200 turns for the same, so I modified a lot of units to upward adjust speed/travel as well carry capacity.  There are 5 tabs in the Unit Modification section and you need to go through each of them.  My modified Scout Satellite moves 4 (vs 2) so it can traverse a map more quickly.

I've added a new unit - Drone - by making a copy of the Fighter and modifying it - it's like a short range satellite.

I've added new units for resources - in addition to the Oilfield (Drain Value under Production Tab), I have a Hydro Facility - land based only, longer production time but Drain Value is higher. 

But you do need to be careful to ensure there's a balance with any change.

You can modify almost every aspect of the  Enhanced Unit set; duplicate a unit and modify it; add new units; add sounds; add graphics/graphic sets for the units; modify Transport Capacity and what units it can carry. modify Combat; modify production; change movement attack odds; modify the text description so other players will know the different changes you've applied. Adding new units, new graphics, sounds, etc. is more complicated, because you will have to have the individual files placed in the proper directories/folders. i.e. Sound files will go in movesounds directory. Images for units will go in unitimages. Plus the game does may not handle  some misplaced files in directories - it doesn't know what to do with them.

My Air Transport (for large maps) has a range of 30  (Movement Range 10 - Movement Speed 3) Carry capacity of 4 units (i.e. 4 IN or 2 AR or 2 IN & 1 AR

My Text Description for Air Transport: default values in brackets

Range 10 (12)
Speed 3 (2)
Movement 30 (24)
Carry Capacity 4 (2)
Base Production cost reduced 26 (36 default)

Helicopter has a range of 20 - Movement Range 5 - Movement Speed 4 Transport Capacity 3 but it can carry a lot more units than the default Enhanced Set.  Make additions under the Transport Tab.

When you make changes in the units, change the default text under the Basics Tab - for 2 reasons - so you know what you changed if you want to edit it again. And if you let others use your revised unit set, the game will show the text changes - IN GAME - press the DB button for any selected unit and it will show the stats as well as the changed text, so you and other players will always have access to that unit.

You can run into problems with carry capacity modification when the unit is damaged vs how much it can carry - so you have to modify the damage level to maintain a similar carry capacity/damage rate as the Enhanced set. So to enhance the Transport to carry 8 instead of 6 (Transport Tab), I also increase the Hit Points 4 from 3 (Combat Tab)  so when it takes a 1 hit damage, it will lose 2 units spaces, which is the identical ratio for the standard unit of carry 6, damage 3. If you increase just the carry capacity to 8 without modifying the Hit Points, when it takes 1 hit, it will lose 4 units. This is an example of how one change will affect gameplay - With the added hit point, it's a bit harder to damage/destroy a Transport. You can enhance the Combat effectiveness of other units under the Combat Tab.  Example from the Combat Tab - Default DE destroyer verses a default Transport - Combat odds = 66%

It gets even more complicated when you have a unit like the Carrier, carrying helicopters that carry units.

The Unit Editor is difficult because every unit is connected and can effect every other unit in the game. It's called a Database because that's exactly what it is...  In the Database Editor there's a button DB near the tabs, whatever unit you have selected the DB will list all of the data for that unit. You can also export the DB data to a file. When in-game, use the DB button to show stats for whatever unit is currently selected.

Save often and test frequently when you first start out. Make a note of all your changes.  I often indicate the default value in brackets in the description so I and other players know the difference between the unit sets. SAVE OFTEN; MAKE SMALL CHANGES and TEST.