The Search Based Keyword Tool is intended for researching keywords within Google’s Adwords network. Unlike the Keyword Tool, the Search based Keyword Tool is based solely on searches from Google.com. This factor causes the search volumes displayed to be considerably lower than the Keyword Tool. Because this tool is intended for paid search keyword research, it contains additional information on Suggested Bid and Ad/Search Share. The Search Based Keyword Tool is seamlessly integrated into the Google Adwords interface and allows marketers to add keywords to their PPC campaigns without having to login to their Adwords Client Center.
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!
It would be great if you can provide comparative analysis of this tool with Google Keyword Planner. Since you’re using this tool so you can provide best comparison. One differentiation which I understood is that this tool works for yahoo and bing as well whereas Google keyword planner works only for Google but Google being a dominating search engine, gives the highest returns, so only this reason may not be enough to buy it.