Here is my two cents. I have used thesis and flexibility as well. With thesis, if you want to make any customizations you have to learn how to code with open hooks. This was a pain for me. I figured it out, but the simplest changes took me a weekend to get right. Not good. There is a lot of support available for thesis, but the implentation of what you are thinking of making the blog look like and then what the results end up to be are quite different. There really is no way around having to learn hooks, have a skin,( like gfonline said), and then figuring out the rest of the code. It gets to the point where it is much easier to hire a designer to complete your theme, which basically ruins the point of having a customizable blog.
Flexibility has great support. I have been a lurker for a long time, and found that Ryan gives outstanding, hands on support.
In regards to the SEO quality of thesis vs flexibility, in my opinion, its a lot of great marketing. Thesis has a nice affiliate program once you own the theme to have other people buy from you which causes a lot of information to push toward that theme.
The kicker is you can have the same quality of SEO with the flexibiliy theme with the help of a few plugins, which are free.
Another takeaway, is that flexibility is easier to teach to someone that is just getting started, thesis has a much higher learning curve due to the hooks.
I don't know what niche you are in or what your end goals are. But personally, I recommend flexibility over thesis for these 4 reasons.
- Easy to teach
- Great support
- SEO is the same with plugins
- Easy to duplicate and scale with clients that want a hands on approach, without draining your time dry.
Anyway, thats my take on it, hope that helps.