On a strategic level the superiority of Nuclear vessels becomes even more pronounced. Even with the 212 long distance stealth is not realistically possible. At least in terms of true strategic distance. It is certainly possible for diesel boats to snorkel but every time they start they are far more subject to being located. They don't have the safety margins for under ice operations and are unable to linger. Much of the strategic value in submarine operations is related to uncertainty. The longer the period of time between last contact and the current time the less certainty there is regarding what areas are threatened or being monitored. Again the Nukes have the clear advantage. On a tactical level nukes have a slight advantage but on a strategic level the competition is not even close.
The effective range of a Nuclear vessel is unlimited. Within a week or so they can be anywhere in the oceans or seas from anywhere. They can do this surprisingly quickly. Diesel boats top speed is significantly slower regardless of their mode of operation. At most a diesels range even at slower speeds is a few thousand miles. This may sound like a lot but considering they will have to refuel at the end it is a significant limitation. There is also a significant logistic advantage to this. There is less or no supply chain to protect. Less risk to re-provision vessels and less opportunities for hostiles to harm support vessels. Again this measure goes hands down to the nukes.
Range and endurance are related but not the same. Staying time on station for a properly provisioned nuclear vessel could literally be months. The advantage this provides has significant impacts to the entire planning, logistics and cost structure of the Navy as a whole. Intelligence gathering missions are more effective and misdirection is easier. Area monitoring and denial are easier to facilitate and more effective. Once more this item goes hands down to the nuclear vessels.
In the long range speed category Nuclear vessels are several orders of magnitude superior to the best diesel vessels. Week long flank runs are possible. Diesels that do flank speed for more than a few days would have to be re-provisioned leading to the limitations mentioned above. In addition to this advantage although I don't know for absolute certain I think that the top speed for nuke vessels is likely to be quite a bit higher than diesel boats.
Area control is a function of all of the items that have already been discussed both in tactics and strategy. In the Navy as a whole a sub is much less effective at this than carriers but they do have one thing going for them. Uncertainty is the subs friend in this area. By stealthily maneuvering and positioning a significant amount of ocean can be denied to the enemy. They also are able to identify and locate objects that may not be easily located by surface vessels. If the submarine is unable to move relatively quickly or opposing forces are able to periodically locate it the entire advantage is lost. It would take several Diesel boats to effectively patrol the same area as a nuclear vessel.
One of the biggest items that advocates of diesel boats attest is their ability to operate in shallow water. Right now it is true that this is an area that nuclear boats are challenged. This is not due to any inherent weaknesses in nuclear power however this is primarily a function of the size of the vessels. It is true that the need for water flow for cooling can be problematic but designing baffles and alternate cooling mechanisms is a far less intimidating proposition than the challenges of designing mechanisms to overcome the weaknesses of Diesel boats.
Overall on a strategic level Nuclear vessels are probably 10 to 20 times as effective as a diesel boat.
Economic arguments are perhaps the most persuasive points in favor of diesel boats over Nuclear subs. I don't know what the current class construction costs are but more than 2 or 3 Billion USD per vessel would not surprise me in the least. It is unlikely that the newest diesel boats break 500 Million USD. This seems to be a very significant difference but as bubblehead points out in this post (more here) there are a number of items that would mean that the construction costs for US boats would be higher even if they are identical vessels. Furthermore if the designs are for smaller and simpler boats nuclear vessels could be cheaper.
Cost of operation is harder to determine. If the same operational tempo and deployment requirements are applied then nuclear boats are likely to be much less expensive. They don't consume nearly as much fuel (the still have a Diesel but it is only used in emergencies and drills). An additional operational cost that isn't often identified for diesel boats is the cost of the cost of the support structure to supply them away from home. More strain will be placed on oilers. Since subs often operate in different areas than surface vessels new oilers are likely to have to be bought. Over a 20 to 30 year lifespan these differences are likely to be pronounced. The need to refuel and the cost of a refueling overhaul probably evens this out however. Decommissioning of nuclear vessels is undoubtedly more expensive and probably costs nearly as much as the construction costs. This one is clearly in favor of the Diesels. Overall Nukes are probably 2 to 3 times as expensive as a diesel sub but since on a tactical level a nuke is worth 3 or more diesels and since on a strategic level they are worth 10 time or more that cost is well justified.
There are many different efforts to make diesel boats more effective. This is great sooner or later something will surpass the nukes. one of these efforts is the 212.
The 212 is a new U boat class that the German navy is building. It has some brilliant innovations that enable it to operate for extended periods of time. Most of the articles I have read place the operational time for the 212 at up to three weeks of submerged operations. This is amazing for a non nuclear vessel (even though it is an order of magnitude less than nukes). I very seriously doubt that it can do 2/3 bell or even the equivalent speed as a nuke boats 1/3 for three weeks however. As brilliant as the 212's use of fuel cells is they are still far away from true nuclear capabilities.
This brings me to my crazy idea. Combine the capabilities of either a hydrogen/oxygen fuel cell or perhaps better yet hydrogen peroxide fuel cell with decay based RTG's. The RTG's could probably be placed external to the hull simplifying cooling requirements. I doubt it is likely that you could ever design an RTG based system that on its own could achieve greater than 4 or 5 knots because their power density and power to weight ration are pretty crappy but you could use them for slow speeds and to "recharge" the fuel cell storage. I'm sure this could get close to fission overall but it might permit something that is in between and might provide a location to get rid of some of the fission "waste" that we currently are unable (by treaty) to reprocess.
Like I said Crazy idea.