Ex-pat Scots, whose nationality will be affected by the result, were specifically denied the vote, while English people and other nationalities, including Germans and other Europeans living in Scotland, have been allowed to vote. Complete insanity.
On your initial question, it'll just be a straight up question of what's more important - a passport that reflects your heritage but that might have more visa requirements for a few years, or retain your existing one. If it came to it, I'd take the rUK one for now, it's not a big issue - it's like all the people I know who're from other countries and also have a UK passport.
Er, no one has proposed that England become independent of the UK -- if Scotland leaves, you could have a Scottish passport or end up with a British passport. The United Kingdom of Great Britain and Northern Ireland -- comprised of England, Scotland, Wales, and Northern Ireland -- without Scotland will still be the United Kingdom of (most of) Great Britain and Northern Ireland -- comprised of England, Wales, and Northern Ireland.