I've discussed subs with HiTech before, and at the time (several years ago, I grant you), he envisioned a "wolfpack" mobile spawn-point that would have a plotted course like surface fleets. Players would spawn a u-boat from it, and control it in a similar fashion to the PT. This would necessitate all new maps, of course, since the terrain below see level would have to be modeled, and the water-air interface rules defined. Such wolfpacks could be sent to patrol off of strategic bases, or in nautical bottlenecks. They would flash when an enemy fleet or wolfpack comes within range, I suspect. Note that even surfaced a u-boat has no chance to catch a fleeing surface warship, though they could and did run down slower convoys. Submerged, they only moved at 3-4 knots, except for short bursts of 7-10 knots (batteries would be exhausted in an hour or less, in those cases). However, they could also be useful once near an enemy base on the coast, as they typically carried a naval gun on the deck in the 3 to 5-inch category. Surface, begin shelling, dive and evade when an enemy plane or PT boat approaches.
One element of arena play would have to be reconsidered, however. Most u-boat action took place at night, for obvious reasons, one of which is that a plane could easily spot a shallow submerged sub during daylight and attack it. I would not use icons at all with subs, but would insure that the wake (either for the entire boat while surfaced, or just the periscope while submerged) was easy to see from a distance. Many more thoughts on this subject, but this'll do for now.