Good question! In your question you've hit upon the key points for why the submarine ambushes did not pan out - technology and command. Both of these are heavily intertwined.

So first lets talk about submarine technology during the war. I've seen the submarines of 1914-1918 commonly described not as "submarines" but as "submersibles" such as in the Smithsonian's "Definitive Visual History" of WWI. They say

The submarines used in World War I are more properly called "submersibles" since they chiefly traveled on the surface, submerging for periods of a few hours at a time...

Or such as in this article by the BBC iwonder division which states

What’s more, they could only be submerged for around two hours at a time

These are what I would call misconceptions and myths about early submarines. The submarine technology available in World War One allowed for submarines to be submerged for 24 hours or more. It would not be the most comfortable 24 hours, but the submarines were more than capable of it. Many in fact did submerge for extended periods of time like that. For example, Georg von Trapp's U-14 (the captured French submarine Curie), was more than able to stay underwater from 12-24 hours.

The submarines of the war were designed to operate and fight underwater. While many would end up being armed with "deck guns", in a battle situation the submarine was a sitting duck while on the surface. Their strength was in ambushing targets while underwater. This worked well when submarines (particularly German U-Boats) were sent out on their own to hunt Allied shipping. It was part of a larger strategy, but one they had a lot of individual lateral freedom in.

Part of the reason for this freedom was the fact it was difficult to communicate with submarines once they were at sea. Radio Signals were easily intercepted and were the primary method of communication that the U-Boats (and other submarines) had with their superior officers. In fact, much of the British intelligence about the U-Boats was based on their daily, or near daily, radio reports to base. The British admiralty, by 1918, was able to effectively plot where U-Boats would be and to station defensive units to either fight or deter the U-Boats.

The British were no different in that their submarines communicated with radio. The other half of radio communications, aside from the fact they were easily intercepted, is that it could only be done while surfaced. The submarine had to be in its most vulnerable position where it could be easily rammed or shelled in order to communicate. So in order to communicate they would reveal themselves both by being on the surface, and through their communication.

I'm rambling a bit, but in essence what I'm trying to say is that the submarines themselves were capable underwater boats. What wasn't capable was the communication technology available at the time.

Simply put, this is why the submarines that were intended to ambush German and British vessels at the battle failed. The British had ordered three submarines to lie submerged until June 2nd. Because they could not receive or send communication, the submarines and their crews were simply not alerted to the battle that was raging, or that they should prepare to ambush German units sooner.

As I had said earlier, these communications were being intercepted by the British Admiralty. Between May 17th and May 28th they had noticed an odd pattern with the U-Boats; many had been sent out but they were not attacking merchant vessels. As a response, the British had sent out even more Anti-Submarine patrols. This would reduce the effectiveness of the U-Boats as they were being hunted by the British to prevent them from attacking the Grand Fleet.

The Germans are a bit more complicated than just communications. Firstly, on May 31st German submarines did alert Scheer to the presence of elements of the British Grand Fleet. These messages were discarded as "too vague". Attempts to attack the British vessels by U-32 and U-66 were made, but the situation proved to be fruitless. U-32 was spotted and its torpedo was dodged. U-66 dived deeper to avoid escort craft (destroyers) and thus missed its opportunity to attack. The U-Boats failed Scheer in both not providing him adequate reconnaissance information, nor did they sink any vessels.

Finally, while the submarines were capable underwater boats, they were not the fastest vessel around. Had the battle been communicated to submarines of either side, the submarines would have difficulty catching up with the relatively high speeds that the fleets were cruising at. Underwater the submarines were slower than on the surface, but on the surface they were vulnerable. Faster than while underwater, but not fast enough to catch up with the fleets. Thus they would be in a very bad spot if they unexpectedly encounter elements of the opposing side's fleet while trying to catch up in order to set up an ambush. To top that off, the battle simply didn't last long enough to facilitate distant submarines to arrive on scene on time. The first hit of the battle occurred at about 14:36 on May 31st, the Dreadnoughts faced off at about 18:15, Scheer turned away 15 minutes later, turned back again at 19:00, and by 19:15 was making his second turn. By 04:15 the next morning the Battle of Jutland was over and the major elements of the surface fleets had only clashed for a few minutes. There was no time for more British submarines to attempt to take up positions, or more German U-Boats to attempt to get involved.

In short, the technology available was not fit for the strategy. The strategy itself was an intelligent one, use your weapons of ambush to ambush the enemy vessels as they unknowingly pass by. But other technological considerations got in the war: Communication and speed. The technology did not allow for effective, minute by minute command of submarines. As well, in the case of the U-Boats, they were in danger from British vessels and lost their opportunities to attack.