Is there a simple way to make these rough sawn, exposed joists level and flat?
The Code requires the floor joists to support 40 psf Live Load (people, furniture, etc.) plus Dead Load (permanent flooring, insulation, etc.).

It appears your joists are about 24” on center (based on the size of the bricks).  Therefore, your joists (rough sized) will support about 120 plf at 13’ span depending on the species and grade. 

If the joists are at 24” on center, then your floor will support about 60 psf (Live Load and Dead Load).  Your dead load should be between 10 psf and 15 psf. So, your joists are adequate. 

However, in kitchens we always add a joist (or 2) under the refrigerator. 

Notching the bearing end “about half way up” is serious. This limits the support strength in “shear” but not “bending”. (Notches in the middle third of the span affects bending more than shear.)

With that big of notches, I’d guess (without actually doing the calculations) you’ll loose about 20% of the total strength of the beam. 

Therefore, you can shim each joist to get the joists level, but I’d keep the added weight (shims) to a minimum and I would not add a ceiling finish under the joists. I’ve seen leveling done with a transit and level, but it’s time consuming. Start at the highest point in the room and work out in all directions.