Having supplied parts for both machines, I can tell you that they both work quite well, and there are many successful builds in both camps. In general, people have had great success with the new rack and pinion based systems on both (the kits aren't officially offered on Fine Line's site yet, but Nate has plans that he has been building 2' x 4' kits with).
They are both cost-effective machines that focus money in the correct proportions to where it is needed.
Both systems offer great support -- you can always ask me about anything related to the FLA machine since it is made with all CNC Router Parts components. Joe's forum is fantastic community support, and Joe does a great job of getting back to people.
It really comes down to craftsmanship in terms of how good a machine you will get -- there is still "some assembly required" with either kit. I personally like working with aluminum extrusion myself, as I like the strength and the flexibility of the system, which is why my parts are designed around it. If you want a custom size, I'd go with FLA. However, you really can't go wrong with either one.
Best regards,
Ahren
www.cncrouterparts.com