Custom species code can allow alot of unique features onto your character you cant normally get ingame. For example in my U2skaarj, and HaloUT models I have coded them to have custom blood decals, and gib meshes. Also some of the creatures in the HaloUT mod have explosion effects if certain bones in the model are hit, as well as spawning of other pawns from one main model(the infection forms).
Also I have attached custom emitters to certain bones on models, like my SweetTooth model which has flames on its head. So its more than just changing species statistics and making them jump higher, you can add nifty effects to your model so it stands out from the crowd of other models on the net.