So it's time to upgrade my son's quad and am wondering if yamaha or honda make a 125-250 with a auto clutch but still have to shift with the foot? Thanks!

 

Yes, Honda has the TRX250X. It operates just like you want, with the added bonus it can be used like a full manual clutch model as well(but it won't stall.) They also have the more utility oriented Recon and Suzuki offers the similar Ozark as well. Sadly I don't know of any other new machines with this option from the big manufacturers. Used you could add the Suzuki LTZ250 as well for recent production models. While you didn't mention Suzuki, these are quality models that are worth a look.