Just a quick update to inform all users that stumble upon this thread now (or at least after today :)); With the new 1.1.0 release, Spring Roo now does support incremental database reverse engineering out of the box. See this release annoucement.
As a comment on the actual question: I don't think either of the two is way better than the other in the actual entity generation, but there is a big difference of course between AppFuse and Spring Roo aside from the entity generation. If you actually need DAO's, this is something that comes out-of-the-box in AppFuse and put partly in Spring Roo, but there is also a great addon for Spring Roo (Hades addon) that does a great job at this, maybe even better than AppFuse. Main reason to go for AppFuse, in my humble opinion, is if you require another Web Framework (ie Wicket. Tapestry or JSF) as front end then Spring MVC or GWT, as these are currently the only well supported Web Frameworks within Spring Roo (more coming though, like Flex etc.). Other reason you might go for AppFuse is if you want to use an IDE with full intellisense and code-completion support, but don't want to use Eclipse (you can use other IDE's, and build works perfectly well with Spring Roo, but due to the AspectJ files, which aren't recognized by Netbeans, other IDE's then Eclipse currently don't do code completion well for the Spring Roo generated/managed files).
But if you don't mind Eclipse (or better even the Spring Tools Suite) and do want to use GWT and/or Spring MVC, I'd recommend Spring Roo. Main reasons to go for Spring Roo is the, in my humble opinion, higher productivity, far better support, far higher momentum and activity, lower learning curve (for quick CRUD app generation) and of course the Rails like command shell from which you can quickly setup and configure your application.
Ps. Note that I haven't used AppFuse actively for over a year, so my knowledge of AppFuse is a bit rusty.