When combined with a hidden nuclear silo, the MP becomes a deadly weapon in the right hands (especially those with big war chests).
If you DO have a hidden nuclear silo, make sure you stagger your nuclear assaults when you start to run out of nukes. That way, when you run out, you can still nuke once per day (provided you have meet the requirements of buying nukes with the MP), and keep your opponents in nuclear anarchy for an extended period of time.
For nations trying to take as much as possible down with them, I would suggest continuing with your bombing runs. 2 bombers combined with the rest fighters will still cause max damage without compromising your air defences.
Also, don't underestimate the power of spies when in a nuclear war. If you can take out your opponents nukes, you can inflict a nice loss on them. Killing two nukes a day equals two less nukes you potentially face in the long run, not to mention the money they lost in the destruction of these unused nukes.
The Manhatten Project should not be used on its own--it should be combined with other wonders (such as the SDI or CIA to prevent the loss of nukes from spying), thus maximizing your potential for destruction. Also, the Manhatten Project MUST be combined with a large warchest in order to reach its full potential.
Also, the chances of reaching peace mode one you resort to nukes is basically nill until you hit ZI. Fighting in cybernations is much smarter now, with staggered attacks etc. When you attack your 3 targets, chances are you'll have to fight these targets AND three other defensive wars.