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.
In addition, you can dig into the paid side of search and find out what keywords your competitors are bidding on, and then leverage those keywords for your own organic benefit if you're not already doing so. Search Metrics does this as well, but I've found SEMRush to provide a greater range of keywords and they save more historical keyword data than Search Metrics.
Keyword Researcher is designed to search the Autocomplete databases of Google, YouTube, and even Amazon.com. That's a lot of keyword sources! As you probably know, if you're building an authority site, or if you would like to become a dominant player in your niche, then starting with a large database of keywords (that your customers are actually typing in) is a powerful marketing tool.
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).