What kind of quilt requires small squares of batting? Are you doing a quilt-as-you-go? If so... can you make bigger squares, like four 4.5-inch squares at a time, which would be 9-inch squares (approximately)?
For me, if this is indeed a QAYG, I compromise between portability and convenience. I can quilt a 12-inch block on my machine easily, so I wouldn't make anything smaller than that. Actually, I wouldn't go smaller than a 24-inch block, but that's just me.
Maybe I am misunderstanding your question completely...