From what I've seen, I would say:
*A better Mart Editor (as mentioned above)
*A better organised Trainer Editor - during the time I did my Gen 2 hack, one of the very few tools available was The One GSC Trainer Editor. It divides the trainers into categories. Ie, all the Silver battles are in a group, all the youngster battles are grouped, etc. You click the group and then the trainer. The Trainer editors for GBA seem to be a mess. Finding specific trainers can be a pain because they're not necessarily near each other.
* A cry resource / tool - there's a tool to insert cries, but it would be nice to have a resource that contained these cries. Even better, a tool that has a list of cries and you can choose which cry is linked to which pokemon. Heck, even just a rom with the offset locations listed for each pokemon would be great.
* A nicknaming tool. It is possible to do manually, but it would be pretty handy if there was a tool that inserted the nicknaming facility into the rom. Perhaps linked to a trainer editor so that you can edit the trainers and the nicknames their pokemon have together.