A service like BrightEdge comes with the biggest costs associated, but its SaaS solution for SEO covers many areas inside of a single ecosystem, including the ability to explore keyword data. This may be a benefit for agencies that wish to reduce redundancies across vendors, but eventually, it is likely that the need for a second tool will present itself as talent and effort levels increase inside of your SEO department.
"Our whole team has a copy of Keyword Researcher, we use it for everyone of our client's keyword research for the 'Long Tail' and we use it every day to come up with blog post ideas and ideas for guest posting. We couldn't live without this tool. I have used every paid keyword research tool under the sun, and this by far is my favorite tool for mining the Long Tail."
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).