If you felt like replacing the Arpeggiator's microprocessor (which is also the Key Scanning and Voice Assigner microprocessor), you can do it with an Arduino. I've done it. It's pretty sweet. I replaced this microprocessor not because of the Arp, but because I wanted other features...
If you do this kind of mod, you'll have total control over the Arp, you can fix any timing issues that you don't like, and you can add new Arpeggiator modes.
If you don't feel like replacing it yourself, I believe that the KiwiSix upgrade replaces this microprocessor, so it's Arp behavior will be different/better, too.
Chip