To the OP - I can confidently say that you will have no problems. Neither Canada nor the EU requires that its citizens enter the country on their particular citizenship (unlike the US, for example). I have many friends who have dual Canadian/EU citizenship and they travel to the EU on their EU passport and back into Canada on their Canadian passport.
The spelling of a middle name is not relevant between tickets/passports/ID cards in this case. There are plenty of cases where Mr First Middle Last actually has documentation that reads Mr Middle First Last etc, so don't worry.
Originally Posted by
SeriouslyLost
Does Germany still have the restrictions on dual citizenship....? Otherwise, as people have said, just hand over both passports at each border crossing and let them use whichever they want.
Yes, although not within the EU. And, as always, there are ways around the others, but none of these issues are relevant in the OP's case.