Like most models, the 1000 bounced around a bit in terms of geometry, features and components. It was simply a matter of reflecting current taste in the marketplace. Miyata's top GT model was introduced in the very late 1970s and marketed in North America until at least 1993. It was probably still in production for other markets, but that's my last year I've tracked down for the US and Canada.
The one big oversight on most 1000 models was the lack of bar end shifters, which it did not receive until 1990.
The 1990 would probably be my personal choice for the most desirable 1000 model. The bar ends are a big factor. But it's also new enough that it has the splined triple buuted tubing, indexed shifting, hyperglide (a must for those shifting under heavy load), 21 gears and low-rider mounts on the forks. It had lost only a few of the desirable features of the earlier models. Most notable was that the 3rd bottle mount had been replaced by a mount for compressed air cartridges. The 40 spoke rear wheel was down to 36. And the internal luighting harness was missing. The last deciding factor, for me anyways, is that it was also Miyata's century year.
Second on my list would be the 1986. It still has the STB tubeset and lo-riders, but also has triple bottle mounts, the internal wiring harness and the 40 spoke rear wheel. But there's no indexing, hyperglide, bar-ends and it only has 18 speeds.
Third chopice would be any other model after 1986, as it would have the spline triple butted tubing and lo-rider mounts. Most of the other desirable feature are easily obtained component upgrades.