I think the concept of simply having the Manhattan Project as a very expensive small wonder that everyone has to build is a bad idea, for two reasons:
-Unrealistic: The initial investment in developing nuclear technology was clearly massive. The subsequent investment to reverse engineer that technology became smaller and smaller as time went on, until the concept of how to build a nuclear weapon became something you could learn at any university or on the Internet. The Manhattan Project represents the acquisition the the theoretical KNOWLEDGE of how to build nuclear weapons, not the industrial capability to actually produce them. (Such as uranium reserves, expensive nuclear reactors and various other equipment, a high tech armaments industry, ect.)
In the real world many nations that have never had a concentrated nuclear weapons program, and have no nuclear weapons, are none-the-less completely capable of building those weapons if they so chose within a very short period of time. These nations already possess the nuclear reactors, scientists and industries to do so. Examples include Japan, Germany, Canada. These nations have this nuclear knowledge not because of personal investments, but because of the massive investment the United States made in nuclear weapons during WWII. To claim that modern Japan would have to successfully undertake a massive "Manhattan Project" in order to gain the knowledge of how to build a nuke is completely silly (Though the process of actually building those ICBMs would certainly be costly).
-Unbalanced: Making it much harder for smaller nations to develop a few nukes really screws them over unnecessarily, and makes them somewhat irrelevant. Restricting the nukes to the big boys makes the diplomatic/strategic landscape much less interesting and less balanced. The top civs already have enough advantages.
If it were up to me I'd keep the Manhattan Project as a great wonder, but I would put in a short lag time on the dissemination of nuclear knowledge. The nation that built the Manhattan Project would gain the ability to make nukes immediately, while other nations would gain that ability after a short interval, perhaps 5 turns. This would give the builders of the Manhattan Project a significant advantage, such as the one the United States clearly gained in WWII. In Civ4 I guess this would translate into having their ICBMs roll off the assembly lines 5 turns early.