As an owner of the MkV GTI that you are interested and after being in my sister's '06 Honda Civic LX and driving it...there's no contest in terms of what's more fun. The GTI still has lots of room for people and trunk space. And you can go fast just by dipping into boost. If you keep it under boost, you can get pretty good gas mileage. Plus, the VW interior is made of higher quality materials than the Civic is.
Cant lose on either, but the GTI is slightly better in terms of value and performance. Only thing is it's more money. But worth it.