I do love this common belief that the issues around the Harrier's wing/engine locations were somehow evidence of poor design. At the time it was designed V/STOL was essentially restricted to single-engine configs because engines (any engines) weren't deemed reliable enough to ignore the unmitigatable risks relating to asymetric engine failures in jet-borne flight. A large number of alternative VTOL mechanisms were tried, but with the materials and technologies of the day the only one that came even vaguely close to practicable was direct vectored thrust, and that meant that the engine had to be placed at the CG so that the trust centre was in the right place with the nozzles down. This inherently means that the engine has to be with the wing in the middle of the fuselage, because traditionally aerodynamicists prefer to have the wing close to the CG as well.
So you have two choices - engine above the wing or engine below the wing. Experiments showed that putting the engine above the wing resulted in bleeding great holes being blasted through the wing when the nozzles were vertical [/sarcasm mode] so Hawker opted for putting the wing on the top, over the engine. That meant the fuselage structure had a large hole in the top, so it needed strong sides and belly structure to compensate. Of course it also needed some strong structure to mount the undercarriage which (again by tradition) is generally put underneath the aeroplane where the ground is expected to be.
So an inherent consequence of the basic requirement is that the engine has to be in the middle of the fuselage with the wing above it, and the wing will have to be removed to get the engine out because it's not possible to create a big enough underside hatch whilst maintaining the required fuselage strength/stiffness at an acceptable weight. This means that WHATEVER we did you would still have to remove the wing to take the engine out.
Now another bit of tradition meant that the main undercarriage also needed to be put just behind the CG, but this space was already taken by the hot efflux from the rear nozzles.The available solution was the bicycle undercarriage with outriggers. Perfectly good solution, but it had the minor consequence that you had to trestle the fuselage before removing the wing. But again, there really weren't that many options within the weight/thrust characteristics of the only available engine. So all of this was just the inherent consequence of deciding to build a V/STOL aeroplane in the late 1950s.
The need to jack the aircraft, retract the U/C and then lower the aircraft was nothing to do with the Harrier. This was only needed at sea due to the restricted headroom available in the CVS hangar deck. The RAF never did it (they just trestled the fuselage), so if anything it was a design fault in the ship rather than the aeroplane.
All the rest of the issues fundamentally traced back to the fact that the MoD demanded the Harrier be a "minimum cost conversion" of a technology demonstrator. The MoD were (as usual) far too short sighted and parsimonious with the funding. In fact they were lucky to get even that, because the bulk of the funding came from the USA and Germany through Mutual Defence Fund money.
Now having said that, Hawker DID come up with a V/STOL design which eliminated most of these issues - the twin-boom P1216. It used a 3-nozzle development of the bigger BS100 engine, and the twin-boom layout allowed the mainwheels to be put in the booms so that the engine COULD just drop down on a trolley. But the MoD decided to buy american instead, so P1216 was cancelled, the RAF was stuck with the Harrier II and the RN was left to suck hind tit with further lashups stretching the Harrier 1 to ridiculous extremes.
I'm a GR9 man through and through (cut me and you'll find KT816 flowing through like a stick of blackpool rock), but if it came to a straight comparison between the GR9 and the F35 I would certainly HOPE the F35 was significantly better - it damned-well should be given that it was designed 50 years later and is more than an order of magnitude more expensive. If it isn't then LM need to be taken outside and shot for ineptitude or fraud!
But perhaps the REAL test should be comparing one F35 with the >10 GR9s that you could field for the same money...
PDR