If you have full root and recovery then you best keep it. If you take the OTA, you will lose recovery and you will not be able to flash any custom ROMs.
BoneStock is great! During installation you can pick your "Aroma" by selecting which bloatware apps you do or don't want. It's fast, smooth, and has everything the latest OTA has.
At this time, with this phone, once you take the OTA you MAY NEVER BE ABLE GET RECOVERY AGAIN! There is a large bounty (over $5,000) to be claimed by whoever figures out how to get recovery after the OTA (or better yet, unlock the bootloader) but it's not an easy thing.
You should preserve your options if you can.
BoneStock gets five stars and 2 thumbs up from me!