Except for some pokemon titles and I think there was one another game no GBA titles use RTC.
That does matter though as you can easily patch the rom using GBATA:
http://www.gbadat.altervista.org/tools.htm and get it working (albeit the clock does not advance during power off like it might have otherwise).
DS roms use the built in DS clock.
GBA code compression is currently not supported but I should imagine it will be added at some point (the hardware setup still makes it very viable) and I hesitate to add it may even be stronger compression due to the increased DS power although you being on an SP will mean this will not affect you.
Personally I am really liking having external memory, saying this the EZ3 is up to 8Gbit now which is load of roms.
The one thing the EZ4 does have is long filename support (the EZ3 uses 8.3 naming).