What, if anything, can be done to improve safety of homebuilt/amateur built aircraft?

It depends.

a) The first question to ask is, "Were all of the 1089 crashes exclusively the result of structural failure?"

If they were, then one way might be to create a niche industry that would provide basic airworthiness inspections to home-built aircraft. For example, a company or service might provide, for a reasonable fee, a standardized battery of tests of structural integrity that, while not guaranteeing the aircraft won't come apart at the seams, would at least provide a means of stressing home-builts against the aerodynamic loads expected for their size and weight, or perhaps compared against a standard, factory built model.

b) However, if the exclusive, or at least the principal causes of the mishaps you've described are not clearly established, then the second question becomes: "Were there any distinguishing characteristics between the operators of the home-built and factory-built aircraft?"

As an example, those who home-built their aircraft might have done so in an effort to save money. Did their financial limits also influence the amount of flight training they'd had (i.e., less training than those who could afford factory-built aircraft)? If so, perhaps a contributing factor - if not a causal factor - was operator inexperience, something that would generally be unrelated to the circumstances under which the aircraft had been built. To put it another way, perhaps the operators of the fatal home-built aircraft accidents would have been at higher risk of mishap to begin with.

c) Other questions worth asking would be, "Was there any geographic distribution to the mishaps?" (a phenomenon known in statistical analysis as "clustering," and one that might suggest an increased risk of misadventure under certain flight/environmental/terrain conditions). "Was there any difference in the time-to-treatment between the the fatal vs. non-fatal mishap aviators?" (which might be significant, in terms of outcomes, if the fatal mishaps tended to occur beyond some threshold distance from emergency medical services, or definitive medical care, secondary to flight operations in geographically remote locations).

A good, and important, question, and one that will probably require some close, multidisciplinary scrutiny before it is solved.

I must say that i would never ever fly anything i built myself. im not stupid. i did buy a homebuilt kr2s that was built by a homebuilder and never felt comfortable flying it. certified planes are built to exact standards so when they certify a c172 they are guaranteeing that particualar model c172 will all be built the same. homebuilders ofcourse have not built any aircraft or very few and i would say they make lots of bad choices and some that will and have killed ie using sub sandard parts. homebuilts built by experienced contract companies im sure have a better track record and i wouldnt mind buying a plane built by a actual company. you may want to look at when the accidents accured. were the accidents happening when the pilot was test flying or did the plane break up in flight were they landing accidents and did the plane have more then 200 hours on the engine and airframe? i did sell the kr2s and bought a mooney and feel much better now

well it could have been the pilot because i don't know much about flying but i do know you need someone from the FAA to inspect the aircraft to legally fly it, so either it was the pilot or they were flying illegally because they didn't have anybody from the FAA to look at it first

People building them need to be more careful and build the planes the way they are supposed to be build.

Not allow 70+ year old retirees to build and fly aircraft?