Pokemon was one of the very few games on the GBA to use RTC (which at the time was an in card hardware extra rather than a core feature of the GBA like it is on the DS) so that was dropped when it came time for the DS cart respins in the EZ4 and the like.
You will need to patch the game but once you do it works give or take the provisos below.
http://www.pocketheaven.com/ph/bubbz/ has the patches as does GBATA
http://www.no-intro.org/tools.htm
Emerald does not have a patch as I recall.
As I understand it real time clock does two things in the game
1) Day/night cycles- certain pokemon only available at night or more common at night (replace night with day as appropriate). Said cycle is about 4 hours for an entire day and night if memory serves (certainly low enough that you might see well more than a day in a single session).
2) Real time events. You can plant berries which grow back in 24 real hours. On an original it means you get to plant something and return the next real life day, on a patched version this means 24 hours game time. Berries are something of a minor gameplay aspect and you always have cheats and I think there is something somewhere for GBA pokemon saves (nothing as fully featured as the DS equivalents mind).
Retail pokemon- not going to happen.
Technical reason and some solutions- the GBA slot of the DS is mapped to the DS memory. Full featured GBA carts do all sorts of fancy things with regards to loading up between power and running a game, older carts like the EZ2 can be twisted to appear as such or simple carts like these expansion packs function in a similar manner if you use the NOR memory. The DS code running components of the EZ4 do have the ability to tie NOR memory to the DS rom it is running but it does not carry across to the other devices not to mention I do not think it got updated for pokemon (the EZ4 was old news by the time this all cropped up and was only getting simple AP patches).
Typically DS games just read the header, see it is there and unlock extra features (such things can also be done with a cheat).
Pokemon goes one step further and tries to read a save. GBA pokemon games used flash memory in various forms, flash carts on the other hand use SRAM which has entirely different access/read routines.
Roms can use pokepatch
http://nds.cmamod.com/nds_downloads/ to read from the GBA slot (initially it was only for the 3 in 1 but cory1492 added a bunch of carts over the course of things).
Likewise if you can dump the save from your retail card you can load the rom with said save, do the deal and flash the newly modified save back*. I am not sure about cheats and save editors but they are also worth investigating.
*you could probably do something similar with a GBA emulator for the GBA side of things. Also note the games that come with the pokewalker are a bit tricky to dump saves from (more
http://gbatemp.net/index.php?showtopic=215641 )
Personally I do not play the games (not to mention I still have an EZ2 should I decide to at some point) so that mini wall of text is the what I have learned supporting the card or playing hacker, you will have to ask someone else for more on the specifics or how to fix issues if that is not enough.