I think a more realistic way to handle amphibious assaults would be to lower(say cut in half) attack power of non-marines when attacking from a transport. Well maybe just lower the attack of fast units(after all it's harder for a tank to roll off a transport, through the coast and onto the beach then for a guy to walk through it) and keep the infantry attack the same, seeing as marines get a boost when amphibious assaulting, or lower the fast unit attack moreso than infantry types. Something like
mobile unit - atk at 50 or 67% power
infantry - atk at 100% power
marines - atk at whatever bonus they get
I kind of sealed off my continent in the game I'm playing right now. Well, I'm playing Archipelagos, and I'm on the top left of the map(huge map, 10 civs). Egypt is about 7 ocean squares south/southeast of me and constantly at war with me. I have two smallish continents(for a huge map that is, about 7 cities worth on one and 4 on the other), separated by one square which i plugged off to protect my northern cities, luckily you can't go immediately from one end of the map to the other norht/south, like you can east/west. I would be screwed then, Egypt's continent is huge(they wiped out the Iriquois so they have about 50 cities or more, compared to my 20 or so). And most of my southern coastline(okay, all of it) is completely plugged with rifleman(I'm in early industrial age), and hell, that is a lot of rifleman, upgraded all the way from spearmen. I have almost 80 total, about half are outside my cities, so about 35 are used to protect coastline and the other 5 are scattered around on key resources or in mountains or whatnot. A lot of those tiles have fortresses on them too to prepare for when they get marines, before I got to railroads my workers had nothing to do so I had them build craploads of fortresses. Sure, Egypt can send tons of frigate/galleon combos around my continent and invade me where I am relatively unprotected, but that gives my ironclads(definately leave several ships spread out among all the sea invasion routes to spot invasions early while you still have time to sink the fleet) time to sink them all. In fact I am in the process of now eliminating a 5 frigate/galleon combo that I would not have time to sink if my southern coastline wasn't defended(they would have landed on my southern coastline). So it was lucky I made that move while I was at peace.
So even if you can't make your island or small continent a complete fortress, fortifying the coastline closest to them is still useful as a tactical maneuver to stall an invading enemy. Provided you start this long before you have to worry about them invading you. I got the Lighthouse so nobody could reach my continent till they got Navigation and could traverse ocean squares cause the only two routes had 3 ocean squares between them, so I just plugged those two pathways with a few ships for the early game and I'm completely protected.
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