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!

Making a list remains hard. And up until a few years ago, doing your keyword research was much easier. You could simply check Google Analytics to see which terms people used to find your website. That is no longer possible. So you’re pretty much left in the dark about the terms people use in search engines to end up at your website. Luckily, there are some other tools which can make your keyword research a bit easier, and could help you speed up the process a bit:
Finding the best keyword research tool also depends on your own experience with SEO subjects such as buying keywords, long tail content, long tail SEO and using low competition keywords. For instance, a newbie looking to use long tail marketing may find something like Long Tail Pro V3 a little too confusing and a bit expensive as it’s a monthly fee and has a confusing interface.

But it’s still very useful for getting search volume data (provided your account still shows this), which is helpful when choosing which of the many keywords you’ve found to focus on (although you should take these estimates with a pinch of salt, they are still useful in indicating the relative search volumes of different keywords, even if the absolute estimates are a little off).
Keyword Researcher is an easy-to-use Keyword Discover Tool. Once activated, it emulates a human using Google Autocomplete, and repeatedly types thousands of queries into Google. Each time a partial phrase is entered, Google tries to predict what it thinks the whole phrase might be. We simply save this prediction. And, as it turns out, when you do this for every letter of the alphabet (A-Z), then you're left with hundreds of great Long Tail keyword phrases.
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.