Probably nothing: England+Wales+Northern-Ireland could still use the Union Jack. (It's not as though there was anything Welsh or Irish in it, anyway.)
And didn't England get the Cross of St. George by borrowing from Malta in the first place? St. George wasn't English.
Personally (having never been across the pond), I expect the Scots to be practical about that, let their cooler heads prevail, and stay in the Union. There are geographic and economic reasons for that; and it's not just the access to roads and airports: it's also the common currency, freedom of movement across the border, and the trade.