If you don't know the difference between head terms and long-tail keywords, let me explain. Head terms are keywords phrases that are generally shorter and more generic -- they're typically just one to three words in length, depending on who you talk to. Long-tail keywords, on the other hand, are longer keyword phrases usually containing three or more words.
ClickBank is the retailer of products on this site. CLICKBANK® is a registered trademark of Click Sales Inc., a Delaware corporation located at 1444 S. Entertainment Ave., Suite 410 Boise, ID 83709, USA and used by permission. ClickBank's role as retailer does not constitute an endorsement, approval or review of these products or any claim, statement or opinion used in promotion of these products.
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!
This isn’t the only tool that mines Google Autocomplete. There’s also KeywordTool.io, but this tool restricts results to ~700 keywords (more are available for “pro” members). Infinite Suggest is another alternative, but despite the name, I’ve found that it still doesn’t find anywhere near the number of keywords that Keyword Shitter finds. And there are tons of other Google Autocomplete miners too. Just Google “google auto suggest tool” for more. There’s also this tool from SEOChat which mines autocomplete suggestions from Google, Bing, Amazon, and YouTube.
The limit on manual keywords could be higher. I personally wish we could input 10,000 keywords at a time, instead of 200. However, I understand the costs that Long Tail Pro has to maintain each time a new manual keyword is input. Not a deal breaker, I just wish the limit was higher. (To be fair, I don't think most keyword tools have a bulk manual option at all).