My first question would be: Do you reload?
If you do, I'd get the Super. It will do anything the 9mm will do except shoot the most common and often cheapest ammo (9mm), but if you reload, you won't care as much.
If you don't reload, get the 9mm so you can not only find cheaper ammo, you can find ammo.
Personally, I think the Super is easier to load for. I have had some crummy shooting 9mm loads, but can't remember a really bad Super load. Kinda like the .38 Spl and 45 ACP, a bad shooting load comes as a big surprise.
I'm another who feels guns are best in their original chambering (and length, and frame material, etc). I also feel that as much as I like them, the 1911 is one of the best examples of that because it doesn't adapt to change as well as some.
However, the Super was designed for the 1911, so it's not much different in my opinion. OK, OK, it was just a hot-rodded 38 ACP*, which was around before the Super, but still.
And it seems to me that John Browning was a fan of .38 auto cartridges. When I have looked back at his auto pistol designs, it looks to me like the majority were .38s of some sort. Maybe I'm reading too much into that, but it makes me think he was a fan of that bore size. And taking that another step, and I'm really speculating here, I wonder if when he designed the 1911 he thought how nice it might be in a .38 caliber and allowed accordingly for a future adaptation.
I don't know. He never said anything to me about it.
*BTW, the 38 ACP was loaded to almost Super velocity at the very beginning, but was toned down. So in essence, the Super was the return of the original plan for the 38 ACP.
And keep in mind if you ever need them for either a 9mm or Super, in addition to using a different ejector and extractor, the firing pin is different. It has a smaller diameter tip, which reduces chances of primer material being squished into the pin opening in the breech from the higher pressure cartridges.