I've been with the SC series for years and years (since the early days of WiE) and have seen this question come and countered before, but haven't seen any recent suggestion, and with the wave of new patches and corrections, I feel obliged to put my case out there again.
Let me present my case before you burn me

Why I think that LR amphibious transports need nerfed:
1. As is the allies can just spawn waves of amphibious forces, from a far away base, and swarm the oceans until they reach an impossible destination.
2. I mean, the US shouldn't be able to sneak marines through the Jap sea, under almost max Japanese naval air cover, to invade Korea. Not without warship escorts. It should be suicidal. As is, its a good gamble.
3. If you have naval bombers with 3+ long range, you should be able to take advanced warning. Meaning, the LRT's movement shouldn't exceed the spotting range of a naval bomber.
4. As is there is no island hoping. No actual need for an invasion base as close as possible to the invasion site. For operation Overlord, the allies where considering Calais, just because it was like 1 "hex" closer than Normandie. In the Pacific they where forced to take the next island before considering the other one. Putting large amounts of men into the sea was always a huge risk.
What I would propose, is 1. to have long range amphibious transports not being able to cruise. 2. Drop readiness for each turn in sea.
Back in the day the main argument in favor of the LRTs, was that without them you cant have things like operation Torch. I'd also propose to make Op Torch an event, where the US spents X mpps over Y turns, to spawn 4 amph. transports (HQ, 2x Corps, 1 Army) near Casablanca.