It all depends on what you want to do with it.

For the 250:
85-86 is the lightest of them all, but requires the most work (like strengthening the frame, swingarm, and engine swap if you want more bolt-on go-fast parts)...fortunately a lot of the important parts are interchangeable or easily modified to accommodate from other years.
87 engine has the big reed intake, theoretically better for drags and hillshooting, uses a different piston than the 88-92, all engines from this year forward have powervalves and a 6 gear trans.
88-92 engine has the small reed, better for MX/trails, reeds are easier to find.
87-90 frame is the full-floater rear suspension, just like the 85-86, but with a stronger box-type bearing carrier for the swingarm, a-arms are slightly different and do not interchange with 85-86 years.
91-92 has a no-link suspension, heaviest of the frames (and supposedly strongest), and some came with nice graphics from the factory.

The best year for the 250 is truly personal preference, and the 87-92's all perform about the same, while the 85-86 engine is virtually bulletproof if maintained at mild power outputs.

For the 500's...
The 87 had different a-arms, big reed intake, 6 bolt head, and some other minor things as opposed to the 88-90.
88+ 500's had the small reed intake and a 7 bolt head.
As with the 250's, all 500's perform about the same...big reed or small isn't important until you're at drag racing power output, and even then some small reeds can put big reeds to shame.
Fortunately, the cylinders are interchangeable provided you have the associated components for them (cylinder head, piston, reeds, intake boot, etc.), and that goes for all of the powervalved 250's as well.

KyleT is a member here who's done extensive research on the subject and can tell you if they used a different grade bolt on the fender mounts between year models if you're interested in that info.


Now, a hybrid is a completely different ball game, as you're retrofitting a 500 engine into a 250 frame (or maybe you want to go with something exotic, like a 500 powered Z400?).
You lose weight by utilizing the lighter frame and thus a hybrid will be faster than an identically powered zilla.
You will need some welding and fabbing skills, along with a hybrid pipe and some of the associated 500 components to bolt on your 250 frame.
Again, which year model 250 frame would be ideal for the conversion is also a personal preference...you want a lot of work, a strong frame, or a quick and easy project?
Big or small reed...again personal preference!
Sourcing parts is also a concern, are you going to pass on a big reed that's within your budget just so you can wait for months until a small reed shows up in your price range?
Would you rather use the frame you currently own, or find a frame that's better suited for you?


TL;DR
They're all about the same, they all have their redeeming qualities, find one that suits you personally because there isn't really a top dog here.

91-92 is more of an RM link. All 3 generations of 250 frames require gusseting of some sort, especially in the debt end.

I read somewhere that the rear shock on 91,92 mounted from swinger to frame.

There it is 

85-86 will take the 87-90 swingarm with very little mod. Insert a 3/16" spacer on each side of the dogbone mount at the swinger. Perfect fit, $1.50 in parts LOL

If you ride dusty areas, go with a foam filter instead of the k&n. K&N allow fine particles through them. I use an UNI with outerwear, and a light filter oiling before every ride.

Never heard any complaints about the performance of the KnN firlter. The issue is dust. Whatever filter you choose, remove it after a dusty ride and check the carb and intake for dust.

If performance suffers from a filter that separates fine particles, it's because the filter isn't sized large enough for the engine.
K&N's biggest claim to performance increase is because it flows more air for a given filter size.
While that's important for guys that want to drop in performance instead of buying or building a larger airbox in their car (or there's not room), it's not the least bit important for applications that aren't restricted in size.
So if filter size isn't a concern, then their performance increase is negated.
Simply a matter of the filter's CFM rating that determines power gains.
If a K&N flows twice the air that a paper element will, then you'll get roughly the same power gains if you double the size of the paper element.
It's not like a K&N filter injects an oily red magical nitrous mixture into the engine LOL

I ran a K&N filter on my 250 for a few hours, then I took it off for some reason and noticed that there was sand and dust coating the intake tube and carb.
It was a brand new filter, and was oiled correctly.
Switched to a larger UNI filter and never saw debris in the carb again.
Never trusted the K&N filter, or any filter for that matter which had holes in the element 5x bigger than the grains of sand and dust that it was supposedly "filtering" out.
Sure, the oil does a lot to trap the sand and dust, but it doesn't do anything for that errant particle that gets sucked directly through that hole in the mesh, completely missing the oil-soaked element.
At least with a foam air filter there's not a direct route for the particles to follow, it has to pass through a winding tunnel of sorts (don't know what else you'd call a path through foam mesh) to get through, and with oil covering the walls of every passage you're a lot more likely to trap that particle in oil.