Fees answer first - yes, the $21 USEA fee is in addition to the entry fee so calculate that into things as well.
As for which event, well I think that would depend on your horse and comfort level. I’ve competed at both events and I’d deem them both pretty inviting. Last year I did both on my more green horse - Jump Start was her first recognized and MTPC was her second, both at Novice. Here are my comparisons on the two:
Footing - You can’t get much better than the KHP for footing! Especially in September, the ground is typically about perfect for JS. That being said, I found the footing at Percy Werner pretty good for MTPC last year. One thing important to note is that MTPC runs dressage on grass, while JS uses the dressage complex at the KHP.
XC courses - I thought both courses were pretty inviting last year, but I also know the builder/course designer for MTPC and what to expect from him in his courses (he also builds/designs for IEA). When JS first brought in the new designer two years ago, the courses were far more beefy than usual for the event, but last year all seemed like usual as a end of season move up type event. KHP has more terrain to the courses than PW and I think the water at KHP is slightly more inviting than the one at PW.
Stadium courses - The ring used for stadium at MTPC is pretty small so expect most lines to be related distances and tighter turns. It was a fun course though - rode very much like a jumper round for me. Warm up is on grass (same used for xc warm up). JS always has good courses that ride well. Warm up and stadium run in the rings east of the barns.
Show atmosphere - I think the KHP has a bigger atmosphere and can be more for a greenie to take in, where things at MTPC are a little calmer.
Facilities - I prefer the facilities at KHP (permanent stabling, wash racks, bathrooms, camping available, etc) over MTPC (mostly tent stabling, no camping/electrical, wash areas in grass got messy). But I also stabled at a barn off site and trailered in for MTPC to save money, so it wasn’t awful.
Show management - Both great in regards to organizers/secretaries. There were some issues with the TD at MTPC last year, but I think they are using someone else this year.
I’m not really sure what else to include… hopefully those notes help you make a decision! I was thinking about doing both events again this year with different horses, but didn’t realize until your post that they were back to back weekends. Hmmm…