First of all, I totally agree that Civ IV should have a straightforward map editor like Civs II & III did. I despise random maps; I
always create my own to play on - I have since Civ II - and having to do it through WorldBuilder is something of a hassle. It's my only real complaint about Civ IV. I just can't imagine what Sid and his design team were thinking when they decided to go the WB route.
That said, it is entirely possible to create fun maps with WB. Here's what I do:
1) Set up a game as normal, using whatever parameters you prefer (I usually do Terra, large map, epic length, temperate, normal sea level). If you care about which opponents you have, select them as well.
2) Enter WorldBuilder as soon as the game starts. Do not take even a single turn. Choose "change all plots to ocean"; this will remove all players and land from the map. You will have to erase some coastline tiles and ocean resources by hand, but this is easy using the 6x6 brush.
3) Cycle through each player and unreveal the entire map. If you don't do this, their original starting position will still be revealed to them no matter where you eventually put them on the map.
4) Create continents and islands as you like. I find that doing a rough sketch on paper beforehand helps a lot.
5) Distribute resources. Be careful to balance resources and land so that each player has a roughly equal start. I guess you could give yourself some advantages, but I advise against it. It's just no fun to "win" a game where all the oil and uranium was on your home continent. If there is some benefit that you really want (e.g., definately having stone and marble), I suggest giving the other civs some small advantage to compensate. Maybe a few extra resources or something.
6) Place the players on the map. Remember that civs who start with hunting get a settler and a scout, while everyone else gets a settler and a warrior.
7) Enjoy!
Doing this for a large map takes me six to eight hours, depending on how meticulous I want to be (even when I'm being lazy my attention to detail is damn near neurotic). And I recommend breaking that up over several evenings unless you like eyeball headaches.
As I said earlier, I absolutely agree that Civ IV should have a Civ III-style map editor. But since it doesn't, the above method, though somewhat painstaking, allows me to fully enjoy the game. It does have one significant drawback, which others have already mentioned: You can't change the civs in the game. But hey, no solution is perfect.
Oh, and if you want a game with an industrious civ, stone & marble, isolated start, I have a WBS that meets those specs. I can PM it to you if you like.