You should be able to taget almost any Nios II system using the "Nios II Generic" target. It does include a number of potentially unused driver packages, however these packages will only build if a device of the appropriate class apears in your SOPC builder system.
For example, even though the generic target includes the CYGPKG_ALTERA_AVALON_LCD_16207 package, this won't be built for your system if it does not contain the apropriate LCD hardware - so there's no harm in having it on the package list.
There should be no problem using the generic target with the UP3 board (although I haven't personally tried that). The only reason you would need to create a new target is if you need to extend the generic package list, for example if you want to add your own flash drivers.
If you have found problems using the generic target, please post them to this forum.