Urn seems to be greater in scope and code. Fennel is intentionally small and a single file that can be dragged into any project.
Fennel does not try to provide Lisp idioms or abstractions unless they have a direct mapping in Lua. For example, there are no linked lists (use tables), and no continuations (use coroutines). Operators are implemented as special forms rather than function literals so that they can be easily implemented efficiently.
Fennel also includes abstractions that might not make sense in a normal lisp but help make interfacing with Lua code easier. For example, symbols that have a dot in them, like "table.insert", have the correct interpretation and can be used as normal symbols. Method calls are supported such via the `(:)` form; `(: "hello" :find "llo")` compiles to `("hello"):find("llo")`.
Fennel takes this approach because Lua is almost already a Lisp, so I felt it was best to add the minimum abstraction necessary. Also, I prefer simple and transparent tools.
Urn may provide more comfortable and "Lispy" abstractions, however, because it takes more control of the environment. It also seems to have pretty great error messages compared to Fennel, and a good website. There are definitely some features in Urn that aren't (yet) in Fennel, like built in pattern matching, although Fennel does do destructuring.