i do both...here's my take.
BJJ is great because it allows you to just focus and improve your ground game to it's fullest.
Shooto is also great but since it involves standup, takedowns and throws, and quick submissions, it makes it hard to focus on just one aspect of the game.
I would say take BJJ first to really understand fully the ground. Once you get very proficient, then join the shooto school where you can then learn to "phase" the BJJ into striking and throwing & takedowns.
I would recommend doing BJJ for reasons other people have given- you will gain more specialized techinical knowledge of groundwork. These days, any decent BJJ school will offer no-gi classes...you can attend these to transition your groundskills for MMA. Best of luck!
the problem with shootfighting is that you don't know who is teaching the clases. In bjj you know who someone is and can easily see his training/background.. Not so easy with shootfighting.