Pain number 6. When we start, the tool was internally built and it was simple to use. Within 6 months, so many people wanted so many features and rules, and it became difficult for me to use. So by doing too many customization, people make simpler things more complex.
Pain 7. Just one manager is not happy about the tool; he/she starts telling bad stories about the tool to others and that creates a bad mindset. So after sometime, people start moving away from the tool.
Pain 8. People keep doing comparison against the best tool in that category with the tool your project uses. A wish list of people kills the spirit. To travel 2 miles to reach office, you do not need a race car that moves from 0 to 70 miles per hour in 7 seconds.
Pain 9. A few people want to try a new tool; for what? They want that jazzy name of the tool to appear in their resume! So the real intention is not to use the tool, but to just see the features and move out.
Pain 10. Ultimate fear of being tracked! Am I being policed? The more details I put in the tool, can act against me. So log only good stuff and let all bad data go to hell. When project is in crisis, and management generates a report, the report looks cool and green with no escalations. But that is not true and everyone knows that.
A tool can be anything from simple text editor to IDE to load testing tool or tracking tool. But people find a way to evade it. But ultimately if the wish matures to need and need turns to be a pain, and the pain cannot be solved without this tool, people do not care which tool they use - they start using it and they stay happy!