Fellow posters, lets not polarize the discussion here because I believe it is in no one's best interest. We are all clever civ players giving our opinion on what we know and speculate about this new game. So, nobody is saying the game will be broken or even poorly balanced regarding this new amphibious feature. Neither it has been said that the previous system (civ iv) was flawless. We all have to accept the fact that what is fun and interesting to some people can perfectly be boring, over simplified or too unnecessarily complex to others.
I personally rather have realism to simplification, having to endure in good terms with tediousness, but I need to assume any degree of modeling a game requires. I was ok with air lift, parachuting, and trade routes as simplified as they were in civ iv, this systems worked pretty fine at the expense of not having tactical game play concerning trade routes, and very little with air combat and parachuting (ranged air superiority, trade routes blockades, etc). For some reason naval logistics/system was given more importance than the above mentioned, I clearly agree, naval might was crucial in much of our world history and it is fun to have it prioritized against trade or even air combat (I believe some people will rather have air combat better modeled for instance). Any ways, ships and army were always "built" separately in reality, we encounter any number of examples of empires having a grand standing army and no navy, and the other way around, transports being a great and important part of the fleets. Taking away transports might be perfectly balanced and may even be "flawless" as we will learn ahead, or it may include any number of new problems which will have to be patched and maybe repatched as previous civ versions showed us to have developed; I incline to the latter here. In any case, the fact that it will be less realistic already displeases me big time, lets hope at least it makes out for an excellent game-play...