What size rear rim should I get: 4.25" or 5.00"?
It comes down to applications, budget and the size of the swing arm. If you can get a 5.0” in there without offsetting the wheel and still leave room for the chain then go for the 5.0”. A 5.0 will make the bike more stable at steep lean angles due to more contact area with the road. You can put more power to the tire in the corner with a wider rim.
Not that you will be slow with a 4.25”, or the bike will be very noticeably under advantaged, however, it is easier to walk or spin the rear tire on a 4.25. Advantages of 4.25 are chain clearance and transition speed from side to side. Tire angle is steeper with a 4.25; your bike will step from side to side faster.
Most of the late model MX bikes will sport a 5.0 without too much difficulty, although they are harder to get in and out of the swing arm. If you plan on changing your bike back and forth frequently from dirt to supermoto you may want to consider the 4.25 as an option.