I'll tell you the issues I've had, bats...and you can just keep these in your back pocket.
For starters, definitely put Sonar 6 on the new machine. It's such a small fingerprint, it's worth it to have just in case, like the others have mentioned to you. Plus, you will have all those old faithful plugs that you will NOT have on the newer Sonar.
Next, go into plugin manager in Sonar 6 and export all your custom plugin saves you may have. You will be able to easily import them all back in and have them if you need them. I have several "good starting point" plug saves that I use religiously. I'd really miss them if they weren't there. You can do this if you use DX plugs as well. You'll see an export option in plug manager and an option that allows you to see what saves are literally in that plug menu. It's pretty cool.
If you are an embedded, per channel Sonitus user, you're pretty screwed. The pro channel change and backwards compatibility are a bit tricky and I hated that whole thing. Though there was probably no other way the baker's could have done this, it's always something that has bothered me. Clicking on the grid sometimes alters your settings in the Sonitus....you know how you double click to see the plug on the channel? That's what I'm talking about.
When you double click, it can alter the eq settings and you can't even see what you touched. Once you open the plug, if you didn't memorize the eq setting, you don't know what moved when you double clicked it. But you'll see the grid change so you know something changed. So any Sonitus eq stuff (the embedded Sonitus) will be a challenge. If you used Sonitus in the bins, you're fine.
Waves: I've had quite a few issues due to updating Waves and them changing either CLSID numbers, (each plugin has a unique number like a license plate) or when I used the Sonar option "hide related VST 2 plugins" due to the implementation of VST 3. So you may be redoing a few things until you figure everything out. Other times, I've had no issues at all.
Lastly, take notice to how your pan laws are set in Sonar 6. This has made quite a bit of difference for me with older projects. Currently, I have Sonar 8.5, X1, X2, X3 and Plat installed on my system. This way I can open old projects that were created in those versions if I really need to. But if you use the pan laws you had for Sonar 6, you'll have less of a chance things will be different. Then again, I believe Sonar has some new thing in it that knows what pan laws were used in an older project and may compensate or something. I know I read that somewhere, but do not know the full story there.
The main issue you will have is anything you do in this new version, will not work as well in the old version should you need to go back. If I can think of anything else, I'll let you know. Good luck with everything!
-Danny