Early game trade routes consist of 1 free one, 2 from lighthouse, and 2 from great lighthouse. I don't know about you, but the possibility of 2 more trade routes before I even get open borders usually doesn't appeal to me as it would tie up my capital for 20+ turns, which I could have instead used to build warriors/settlers/workers, which to me means that the great lighthouse isn't an early game wonder except in the time in which it appears.
So that means that you'll have 3 trade routes, and +50% from harbor, +25% for connection to capital, vs 1 +25%. Woo hoo, you managed to snag 4 more commerce from your city than an inland one would have, for the price of 2 buildings, and food resources/fishing villages for 30 hammers a piece. If you have 1 resource, 2 fishing villages, and 90 hammers for the harbor +120 hammers for the lighthouse, thats 300 hammers spent on getting this city what it needs. 1 worker costs 90 hammers - so you could get 3 workers and a warrior for the price of setting up this one coastal city, or 5 axmen. Now, will your coastal city produce more commerce? I sure hope so after that investment. Will it produce more hammers than an interior city in the early game - probably not, as it is working three water tiles, only two of which produce a hammer, and it would only be able to work 2-4 inland squares in addition depending upon how many happy resources you have managed to find, as opposed to another city working 5-7 inland tiles, which in the early game we can once again assume that at least 2-3 of them are resource tiles (otherwise, we need to have a talk about your city placement scheme).
Lets look at this in another way - what if you are going for a conquest style game instead of a builder style one. You just spent 300 hammers on setting up the beginnings of your trade network. I just spent those 300 hammers on warriors - I have 12 more warriors than you would assuming equal numbers of hammers. Or if I spent them on axmen, I have 5 more axmen. Great lighthouse costs 300 or 600 hammers? Once again, 12-24 more warriors or 5-10 more axmen. So for the cost of your building costs you wiping out your nearest neighbor and doubling the number of cities that you have (potentially). This larger industrial base then moves into gear, makes more workers/economic buildings, and proceeds to trudge after you technologically. Your builder style might have an early lead, but double the number of cities, with the right civics/tech path will catch up rather quickly.
If that is the comparison, were those early game trade routes really worth it comparatively?
Now, all that was just addressing your first and third points TowerWizard. Your second point however depends entirely upon city placement. In the early game, most starts will run into a happy cap of around 8

or so. A higher happy cap will generally then depend more upon expansion or the construction of buildings, leaving further expansion to the midgame. Secondly, the concept of reduced gain that you brought up. Every single inland terrain can be improved, with the sole exception of mountains. A coastal tile can only be improved in one of three ways: kelp (not under your control), resources (again, not under your control), or fishing villages. This means that a city can get 1-4 tiles that produce +1 hammer, +3 commerce, and everything else is solely up to the whims of city placement. An interior tile (say, tundra), can be improved with a farm, a cottage, a workshop, etc. Then later, it can be scorched into a plains tile (if you have improved terraforming on). This means that by midgame, that tundra tile can be a plains tile with +2 food or +1-5 comerce, etc. Comparing this to a coast tile, the coast tile will be producing enough food to feed itself and 2 commerce (3 if financial), with no way of further upgrading it beyond what it started out as.
This all means to me that the only possible way that a coastal city could be considered OP is if it was one of the rarely placed ones with 4 coastal squares that you can get 2 fishing villages and 1 resource one. Why? Because with enough workers and a few adepts, every single interior tile not taken by a mountain will produce far more than a coast square. Are these cities OP? Maybe. On the other hand, they are also rare, and will form central points for your civilization, and every civ has major cities and minor cities.
-Colin