I'm not sure about that. I think I'll wait for you to upgrade to MS-II to tell me which was easier.Piggybacking with the factory PCM and only having to tune for fuel sounds easier, but I'm pretty sure that I would be driven to madness trying to tune it while wondering if the factory PCM was somehow interfering as I went.
Trying to keep the factory PCM happy is something I want to avoid entirely. I plan to run the MSGPIO for transmission control when it's ready for release - assuming I have the engine running on MS-II by then. Not a practical option for you guys running newer cars with ABS and traction control though.
Congratulations on getting your build up and running BTW !