I'd agree that a few improvements should be able to go on tundra and desert tiles, like cottages and workshops, but they are otherwise useless and probably should remain that way. I couldn't imagine getting any serious, sustained food yields out of either, for instance.
And tundra is capable of supporting cottages if it's on a river (probably some reasoning behind that), and with lumbermills and mines on appropriate tiles (desert, too, for mines). So, they're not completely unusable, just undesirable.
Do you want tundra to be equal to plains or something? One food, one hammer? Able to support farms, despite the fact that there'd be virtually no food yield with such long winters? Deserts are pretty useless in reality. Yeah, you can throw a city (cottage in game) up on one, but that usually requires a good water source like a river (floodplains).
If you really want to, though, you can easily mod the game to your liking in the assets\xml\terrain folder. Less than 45min, I've done it plenty of times.
I like the fact that many tiles are useless. Resource scarcity is a huge factor in reality, and the game mirrors this well. The best analogue is that a "city" in civ4 is about the size of a small country in reality, maybe like El Salvador or Cambodia or something (check the Earth map to figure it out). Some countries just have little to work with in terms of land, and end up having rather large areas that aren't really worked at all. Dense jungle, arid deserts, mountains, permafrost, etc. They can make up for this if they have a good resource, though.
I think perhaps where the game is most off is in resource trading - you should be able to get a lot more gold out of the deals, and it should increase somewhat in relation to the inflation mechanism.