There are a few misconceptions in your question. Firstly, many of the Royal Navy's losses were not in open water. Antelope and Ardent were both hit and sunk in Falkland Sound, close to land. Coventry was sunk close to Pebble Island, while Sir Galahad was bombed in Bluff Cove. In all of these cases, Argentinian aircraft could attack with their approaches masked by terrain, either in part or in full. The only British ships to be sunk in open water were Sheffield and Atlantic Conveyor, both sunk using Exocet missiles. The other misconception is that the Pucara was rarely used in attacks on ships. The Argentinians only deployed 24 of these aircraft to the Falklands. They were mostly used in ground attack roles. The extent to which this is true is demonstrated by the fact that the Royal Navy's surface ships shot down no Pucaras, while the British Army shot down two, the only class of aircraft for which this is true. Attacks on ships were mainly carried out by A-4 Skyhawks, IAI Daggers and Dassault Mirages, with a scattering of other aircraft, such as the English Electric Canberra or the Dassault Super Etendard.

The main reason why the RN was vulnerable to attack by Argentinian aircraft was that it was poorly equipped to fight the Argentinian threat. The RN of the 1970s and early 1980s was built and structured to fight the Soviet Union. This was expected to involve fighting a Third Battle of the Atlantic, defending merchant shipping in the Atlantic from Soviet attacks, as well as supporting NATO movements in Norway and the Norwegian Sea. Doing so would expose the RN to a particular set of threats in the air; large supersonic missiles, long-range bombers, and nuclear weapons. The RN would also be fighting alongside forces from other NATO nations. This set of expectations dictated how the RN built its ships, the capabilities it developed, and how it trained its crews. Weapon systems like Sea Dart and Sea Wolf were built to engage Soviet bombers and the missiles they launched, respectively (here I'm using 'weapon system' to mean the missiles, the radars used to detect targets and guide the missiles, and the computer systems that tie the two together). Ships were built with uncluttered decks to allow for easy decontamination in the event of nuclear fallout; this meant that ships had few light AA guns. The RN retirecd the conventional carriers Eagle and Ark Royal in the 1970s in favour of the Invincible class of light carriers. These had better capabilities for helicopters, highly useful in ASW operations, but could not carry larger aircraft. As a result, the RN lost its organic airborne early warning (AEW) capability; this was to be compensated for by shore-based aircraft, or by those from other NATO powers. The RN also lost its large, fast interceptors like the Phantom in favour of the smaller, slower Sea Harrier, under similar assumptions.

The Falklands War reversed every one of these expectations. Argentina had none of the capabilities that the Soviets did; no nuclear weapons, no large bombers, no high-flying supersonic missiles. The RN was fighting alone against a threat that it was fundamentally unprepared to face. Decisions that made sense in one context were proven to be incorrect in this new context. With no early warning aircraft, and only the relatively ineffective Sea Harrier as a fighter, the Fleet Air Arm could not easily intercept attacking Argentinian aircraft before they approached the fleet. Sea Dart was designed to target high-flying Soviet bombers. As a system, it was bad at engaging small low-flying aircraft like the A-4, with a number of failures to fire as a result of poor radar locks or computer crashes. It was quite effective when used to engage high-level targets - while hit rates were low, this was because typically two missiles were fired when engaging a single target. Sea Wolf was designed as a pure anti-missile system. On multiple occasions, it failed to engage aircraft targets that were manoeuvring in ways that missiles didn't. Designed to engage supersonic Soviet missiles, which flew at relatively high altitudes, there may have been a number of occasions when the system was confused by waves and shell splashes. The older Sea Cat missile could be used in most situations, but was inaccurate and rarely effecitve. The lack of light AA guns, meant that it was hard for ships to engage aircraft that made it past the missiles. While many of these were jury-rigged onto ships, they lacked effective fields of fire and fire-control systems. As a result, the RN's defences against air attack were flawed at every level.

Part of the RN's unpreparedness for air attack came form the expectation that technology would allow ships to defeat aircraft. The RN had been taught the opposite during WWII, with the loss of Force Z being the clearest example teaching this. However, the loss of institutional knowledge during the years between them, and the increased confidence imbued by the rise of surface-to-air missiles (SAMs), meant that the RN made several attempts to do so. The clearest example of this was the Type 42/22 combination; this attempted to form a SAM trap for Argentinian aircraft using a Type 42 destroyer with the long-ranged Sea Dart missile and a Type 22 frigate with the short-ranged Sea Wolf. In theory, Sea Dart could catch any Argentinian aircraft at high altitudes, while Sea Wolf gave close-in defence at ranges Sea Dart could not cover. As it happened, though, Sea Dart and Sea Wolf could not catch every aircraft. Even when the systems worked perfectly (or near-perfectly), aircraft were still able to get through. This is shown by Glasgow and Brilliant during the first attack on the 12th May. Four aircraft attacked the two ships. Sea Dart refused to engage, and Glasgow's 4.5in gun jammed, but Sea Wolf was able to engage. Two aircraft were shot down, and a third flew into the sea while avoiding another missile; the fourth got through, and dropped a bomb that nearly missed Glasgow. Later attacks on 42/22 pairings, where Sea Wolf failed, resulted in the loss of Coventry and serious damage to Glasgow. The RN's overconfidence in its systems led it to put ships into positions where they could easily be attacked and ovverwhelmed.

The Royal Navy in the Falklands had a complex command structure. In overall command of the British Task Force was Admiral John Fieldhouse, based at the RN's headquarters at Northwood. In the South Atlantic, the Task Force was composed of four separate elements: the SSNs (designated TG 324.3), the Carrier Task Force (TG 317.8), the amphibious group (TG 317.0) and the land forces (TG 317.1). Each of these had a separate commander. The SSNs were controlled from Northwood, while the other three were commanded by commanders in theatre. Rear Admiral John Woodward commanded TG 317.8, Commodore Michael Clapp commanded TG 317.0, while TG 317.1 was commanded by Brigadier Julian Thompson and Major General Jeremy Moore (after the initial landings had taken place). Each of these three commanders was, in theory, of equal status, despite Clapp and Thompson being of lower rank than Woodward. This command structure led to clashes between commanders. An example of the problems this caused is the Bluff Cove disaster. Here, two landing ships, supporting a move forward by 5 Infantry Brigade, unescorted and unprotected by a combat air patrol (CAP), were attacked by Argentinian aircraft. One was sunk, the other heavily damaged, and heavy casualties sustained by the troops aboard them. Tension between the commanders greatly contributed to the disaster. Woodward, who wanted the troops to move forward by foot and helicopter, believed he had made it clear to Clapp that moves forward by ship were too dangerous to make. Moore, meanwhile, did not have the helicopters spare to move the required forces forward and did not want to exhaust his troops with a long march, and thus pushed for ships to be used instead, even one of the large and vital Landing Platform Docks (LPDs). Clapp had to square the needs of the Army with the pressures imposed on him by Woodward, and, as he had little control over the RN's destroyers and frigates, could not provide an escort for any ships he moved forward. The confusion generated put two ships and hundreds of men into an exposed position.

Woodward, and his staff, also considerably micromanaged the work of the air squadrons aboard Hermes and Invincible. Woodward was a submariner, and had never served commanded a carrier. He had relatively little understanding of the capabilities and flaws of the Sea Harrier. This meant that his micromanagement was flawed. As a result, it can be implicated in the loss of Sheffield, and the heavy casualties suffered by RN escorts in San Carlos Water. In the former case, Sea Harriers on combat air patrol (CAP) were diverted to carry out a visual search (as opposed to a quicker radar search) for surface shipping, creating a gap that the Argentinian Super Etendards could exploit. The latter was caused by instructions from the staff keeping CAPs from 800 Naval Air Squadron over San Carlos at high altitudes, preventing them attacking the Argentinian aircraft until after they had released their bombs. A commander more familiar with the use of aircraft would have used them much more effectively. However, they would not have been at their full effectiveness, due to the lack of AEW aircraft. Without this capability, the FAA squadrons had to maintain a CAP in the air throughout. This restricted the extent to which Sea Harriers could be released for strikes and other actions. It also meant that the CAP could be caught out of position, rather than being directed to the most pressing attacks. The lack of AEW aircraft meant that Type 42s had to be deployed forward as radar pickets, exposing them to threats. Coventry and Sheffield were sunk on such duties, while Glasgow was damaged.