I'm friends with the lead developers of both, so I recommend you try them both and choose which fit your needs the best.
That said, Kunena is very strong for community like forums and got more support from template vendors like JoomlArt, while Agora is very strong for support style forums with features like reply by email.
1. With the 1-click migrate solution back to NinjaBoard would this preserve all the forums and settings or would I have to rebuild?
All your data will migrate, except for global settings. Per forum settings will migrate, but not the global preferences.
This is because Ninjaboard differ a lot from Kunena and Agora in features. They have many features we don't, and we have many features they don't.
2. Based on NinjaBoard delivering the features we require say in v1.2 how does NinjaBoard compare to Kunena or Agora?
Me being both a designer and coder means that features you find in Ninjaboard have a stronger focus on design than our competition got. As good design isn't an afterthought, but a vital part of the developing process. The other Ninjas share my point of view on the importance of giving both code and design a balanced focus.
So our features are better looking and better thought out because of how we think and our vision for Ninjaboard.
And because of our competition, we allow ourself to raise the bar on server specifications, making us focus a lot on the higher end market.
And since Ninjaboard is used on several major Joomla sites, like JCE, Akeeba Backup and others things like performance is extremely important to us.
And secondly, Ninjaboard is built on top of Nooku Framework. Nooku is the new kid on the block regarding PHP frameworks, and is by far the best one using more bleeding edge technologies and implementing the best PHP coding patterns in the industry.
That makes the codebase in Ninjaboard the most modern and maintainable of the forums available today.
Thirdly, we take things like icons seriously. Every icon in Ninjaboard is hand picked. The topic icons is even made by a Mac icon designer we hired, made specifically for Ninjaboard that you can use for free! Making your forums look very professional and polished.
And finally, security isn't an after thought either. Several of the Ninjas (including me) have a hacker background, so we test our code for security vulnerabilities as we code, not as a second step.
We also hired Jeff Channell (the best Joomla hacker in the world, best hacker I know personally) to do a security audit to find vulnerabilities we missed.
We'll likely hire him again soon for a checkup just so we're on the safe side.
The new features in 1.2 will make Ninjaboard fill in the void regarding features that we miss today, but many site owners today simply can't be without. That doesn't necessarily mean we're behind the others in general. We have many features they don't, like the ability to set a custom display name per user, built in gravatar support, Chameleon auto skinning template etc.
So that's how Ninjaboard compares in my personal opinion. Naturally my opinion is biased, so I tried to keep my answer as objective and factual as possible.