for emerald, you'll basically be unable to obtain a shiny pokemon unless you aim to get one in frame perfect time, which is hella difficult. cant remember if that applies to ruby and sapphire as well, but it definitely applies for emerald, at least.
you'll also be unable to get regice and you will be unable to go to mirage island, as both are time-based events. you can basically work around all of these with gameshark, so either you could replace your battery (or get Nintendo to replace it at the cost of your save file, if they still do that) or you could just skip the middle man and use a third-party device, since thats the only other way of getting those things to work.
if you're working on a nuzlocke or something i suppose you could just give yourself an extra encounter in the nearest locations?