The primary difference is that Long Tail Pro is a big time saver over MS. With Long Tail Pro you are able to enter in multiple seed keywords at once (rather than just 1 with MS). So, instead of entering in 1 seed keyword, waiting five minutes, then going back and entering in one more; you can enter 5 seed keywords (for example), hit generate and then see all the keyword ideas at once!
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As for the history of the company, as I explained, I created Long Tail Pro back in 2011.  At the time, I was creating tons of niche sites and was doing alot of keyword research and content creation.  I was trying to figure out what types of keywords would rank quickly in the search engines, specifically Google, and I was frustrated with the other keyword research tools (in particular Market Samurai) out there.