AFAIK, none of the available vmu app's support DCI files, you've to convert .DCI to vmi/vms before you can use 'em.

Actually the .DCI format it's pretty simple, although it has the data byte-swapped and has to be correctly swap-back before saving to the VMU.
For my future VMU Tool I'll work first on good save/load routines that support .dci, .vmi, .bin/.dcm dumps, etc. After I've that working fine, I'll work on the "neat" GUI.

About the command line tool for DCI <-> VMI/VMS, that should be quickly doable. I can't guarantee it, but I might work on it this week if I get some free time.

btw, if you want, add your Resident Evil 2 rip to the Dreamcast Rip Database!