It'd be wonderful if some resourceful programmer cleaned up the ROMs so they'd run better on the ED64. I'm sure there are many others like me out there who want to own the iQue games for their historical relevance and novelty.
Don't quote me on this, but I've tried to keep an eye on developments on the iQue front. Maybe someone else can chime in if I'm wrong on anything. From what I've read, the iQue is a lot more powerful than the plain N64. So getting games to run as smoothly on the ED64 as they do in emulation or on the iQue probably isn't going to happen. It's possible that they fixed some bugs which sped things up, but more likely that they just threw more resources at the problem.
I do have some experience with looking at the save issues. I took a look at the 2 Zelda OoTs when they came out. The save code is buried in the main code for the game, and they tore out huge chunks of code to put in the iQue code. You see the N64 uses different code for accessing SRAM, Flash, EEPROM, and Controller Pak saves. The iQue got around this by having a separate program running in the background to handle dumping the save data to a spot in the upper area of the Expansion Pak, and then having the game grab the data from there.
While technically you could redo the code back to the old way, it will be a huge pain. Just for one game, since each game handles things differently.
It might be simpler for the ED64 to mimic the iQue code. Then again, the iQue has more resources available to run a secondary program in the background. I think we may need to know more about how the iQue does stuff first (there are people working on this part).
By the way:
Dongwu_Senlin_CHN_iQP-SUXXORS - Animal Forest
iQue_Mario_CHN_iQP-SUXXORS - Mario 64
Mario_Kadingche_CHN_iQP_REPACK-SUXXORS - Mario Kart 64
Mario_Yisheng_CHN_iQP-SUXXORS - Dr. Mario
Shuishang_Motuo_CHN_iQP-SUXXORS - Wave Race
Xingji_Huohu_CHN_iQP-SUXXORS - Star Fox 64
Yoshi_Gushi_CHN_iQP-SUXXORS - Yoshi's Story
Yueye_Motuo_CHN_iQP-SUXXORS - Excitebike 64
Zhi_Pian_Mario_CHN_iQP-SUXXORS - Paper Mario
Zuhe_Jiqiren_CHN_iQP-SUXXORS - Custom Robo
Zui_Yu_Fa_Diqiu_De_Jicheng_Zhe_CHN_iQP-SUXXORS - Sin and Punishment