Steal.js is about making common workflows easier.
It has an automatically loaded configuration file. Write a big app with multiple pages and this is a huge benefit.
It allows you to more easily switch to a production mode.
It comes bundled with CSS and Less automatically (which also build correctly with steal-tools).
I would love to have System.js support these features, but it currently does not.
The EJS/stache plugins can not be made without the buildConfig option that steal supports. This is so build dependencies can be swapped out.
SystemJS's builder allows shared packages, but does not bundle automagically. There is a huge difference between how steal-tools builds bundles and how SystemJS does it. Steal-tools intelligently creates bundles to optimize caching vs script depth. SystemJS you have to write them out individually. You can do progressive loading, but not automated like steal-tools will do it. Switching to production with progressive loading will also be tricky with SystemJS. You will have to write out a lot of config.
Also steal-tools is written without hacks to the System loader.
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