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what is most important issues and cautious we have to do before upgrade to MySQL 6.0?

How do you do the upgrade? setting up a new slave and do yum upgrade? what is the best way to upgrade with minimal downtime?

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Moving to MySQL 6.0 is highly regarded as a bad move by most people, as it only briefly existed on the control version system of MySQL A.B. plus some very unstable alpha releases. MySQL 6 promised too many features to be able to be delivered, although some of its features were later ported to 5.5 and 5.6. Others, like SQL-layer foreign keys or the Falcon engine never saw the light. The order is more or less: 5.0, 5.1, 6.0 (not released), 5.4 (not released), 5.5, 5.6, 5.7 (not yet released)

You can watch the story by yourself, recounted in first person by a former employee on this video.

Regarding the upgrade (assuming you really meant 5.6), having a minimal HA setup is a must. I wrote a more detailed guide on a previous question, but every setup is different, and all potential problems are too many to summary in an answer, even between 2 specific versions of MySQL.

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MySQL 6.0 does not exists. The latest version that is in production is 5.6.21

MySQL 5.7.4.

I am not sure what version are you using today. But if you are not using 5.6.16 and up you should upgrade.

Even Facebook are working on upgrading form MySQL 5 to MySQL 5.6 as it is the most power full version yet. MySQL 5.7 have a lot more improvements but it is still buggy so I would not put in on a production system yet.

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