I think I'm right in saying the FA2 was hard pushed to do a vertical landing let a lone a take off in many conditions. In the Gulf and the Adriatic the air temp afected the available thrust to the point where four AMRAAM was a bit much to be lunking around if you wanted to settle down comfortably.
Of course if the FA2 had been given the engine that is now in the GR7A and 9A, that would have been less of an issue. However, the GR airframes are rather different to the naval ones; The RAF got the Harrier upgrade that McDonnel Douglas did for the USMC back in the eighties- bigger by a couple of inches all around and a girt big wing on it too. In many ways they got a better plane than the US did, with the extra sidewinder rails and night attack capabilities from the start. However, once they had this plane, the comonality with the RN aircraft was pretty much out the window.
The Harrier 2 as it was sometimes known is a decent ground attack aircraft, but for various reasons, mostly aerodynamic, it really isn't as spritely a dogfighter as the FRS1 was. So, when the RN came to eventually upgrading it's harriers for two main reasons (cost and flight envelope) they stuck with the skinnier, older design. In point of fact virtually all the FA2s were rebuilt FRS1s, and apparently there are only two or three airframes that didn't get converted. There were a handful of new builds too, but even so, the new plane was a flawed gem.
The original idea had been to carry four amraam, and no guns, with two amraam under the fuselage. It turned out that these two rockets got a tad warm when landing, and were getting cooked. It's probably only down to the miracle of modern inert munitions that a FRS1 didn't shoot down an aircraft carrier during the Kosovo crisis.
When JFH came along the costs of trying to support two radically different types on the budget allocated for a single type force proced crippling. A decision had to be made- which one to keep. Right now, the one that delivers the most good is the GR version, so for better or worse the decision was made to drop the fighters.
Short sighted? Probably. But sensible, yeah, just.