I guess it depends what you mean by software raid issues.
I would be amazed if any software raid implementation could be broken by performance differences of the raid components. What I'd expect to see is the performance being hindered by the slowest component in the array.
You haven't gone into what raid types you'd use for all this. Given it's a backup of a backup is it so wrong to just JBOD all your disks together?
Perhaps you'd JBOD the smaller drives to 3TB and then use two new 3TB drives to create a 3 x 3 Raid 5 array (6TB available). I'm not convinced such a system would be a good idea because at what point to you determine the JBOD array element is a bad idea? After it fails once? After it fails three times? Until you run out of smaller drives? What's the probability of any of the hardware raid controllers failing? What would you do if one of these did fail?
You need to weigh up the cost in terms of configuration time and frame of mind with the cost of just buying new equipment.