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!

In a nutshell, Long Tail Pro helps you quickly find keywords in bulk based on a seed keyword that you input.  In addition to returning hundreds of related keywords, the tool also shows search volume (monthly search volume), advertiser bid, number of words, rank value, and my favorite Keyword Competitiveness (helps you judge the competition and keyword difficulty).