I have a good running 87 lt250r motor in a nice 88 frame. I have an 88 motor in need of a complete rebuild. I plan on just rotating engines as one needs freshened up that way I always have one on hand. I know the 87 has the larger 5 bolt reed cage. The 88 has the smaller 6 bolt. Why did Suzuki do that?
Which motor has the best power, and which has the most potential?

Yeah. That what I'm thinking too. My 87 has plenty of low and mid for me, and pulls real hard up top. I'm not sure what work has been done to it. It shows 165psi compression, so I'm just gonna leave it alone for now, but I didn't want to sink a bunch of money in my 88 motor if it's better spent on the 87.

6 bolt is better for low and 5  bolt more peak. Just depend on what you want to race wise.