I test drove both & went with the Bernina 350PE. The feet are very easy to get on/off and Bernina's precision, in my opinion & experience, is unmatched. In addition to the parts that came with the machine, I bought a $19 Patchwork Seam Guide. It is a metal piece that easily screws into the machine bed to make a straight edge upon which my fabric runs so I keep a perfectly consistent seam. I like it so much better than the 1/4" feet with a build in guide. I can set it anywhere from 1/4-7/8" so it's perfect for standard quilting seams, 1/2" flannel seams & even 3/8" sewing seams for my home dec hobby.
It's not a huge deal to switch to the walking foot & honestly, when I tried putting a quilt sandwich through the regular foot with dual feed, it had issues & I had to add walking foot anyways so for me that wasn't as much of a "bonus" as I had assumed prior to test drive. I really, really loved the knee lift on the Bernina & that was a major factor in my decision as it both saves time & helps with accuracy.
Other than cost of Bernina parts, I am thrilled with my machine... but that's my experience based on how I sew & quilt. I would really recommend taking them both for a test drive with your fabric & batting to see what you prefer. The other benefit of the Pfaff is that it's harp is larger. If you plan to SID something larger than a Twin, the 5.5" harp on the Bernina might pose a problem for you depending on your batting.