The wheelbase for all years is almost the same despite the 88/89 have 1.25 inch shorter swing arm.
This doesn't appear to be the case. My OEM Honda service manual list the wheelbase for 86/87 as 51", while "after 87" is 49.8". I know I have heard multiple times over the years that the +1 forward arms were a later model thing for the 250R, but it sure doesn't look that way to me. The wheelbase numbers tell me the only difference between the early and late model years is the shorter swingarm on the 88 and 89's. (If the 88 and 89's did have forward arms, the wheelbase would be about the same.) Also, just about every 250R arm out there is +1 forward, I see very few +0 forward. Seems to me if they years were different, you would see two distinct a-arms styles, +1 forward for 86,87, and +0 forward for the 88,89. You don't see this, so someone can show me a side by side comparison between the two years, all a-arms are the same as far as I am concerned.
As far as handling differences, as RyanWsly stated, forward arms put more weight on the rear. My a-arms are actually adjustable between +1" forward and +1/2" forward, but I have only ever ridden the quad with them in the +1" forward position. One of these days I plan on trying the +1/2" forward to see what difference it makes, but my 250R hasn't been ridden in over two years now, so one of these days I may get to it. As far as what arms to run, since the majority of 250R a-arms are +1 forward, I would go with the +1 forward option. Since that is what most of the are, seems the aftermarket as already figured out what works best. That being said, the best option would be to buy both a +1 forward set of arms and a +0 forward set of arms and test both of them and see which one you like best. Of course, this is an expensive option, but it is really the only way to see what works best for YOU. Since that is probably not an option, I would go with what seems to be the aftermarket standard, +1 forward.
Doug