Yes.You CAN use your 1024 Cart with any MK3.
I had a more in-depth post for ya,but it was waaaay too long.
To the point:you will have a little bit of extra"stuff"if you get the MK3 2006.(512)Throw it away if it bothers you.Or get another MK3 later,start a second set-up for 2player........
You will have the gear I have(paid for every bit of it,worth every penny-as I said,I'm not selling you anything),and I am a really freaking happy dude lately.
The reason I suggest NEO(just figured this out)is,in the long run,I think it will be the easiest(i.e.-no patching)and most versatile equipment out there.