Barroso has been the president of the European Commission since 2004. It is one of the most powerful positions within the European Union political structure. The post of president is not chosen by the people of Europe, but is chosen by vote from the members of the European Commission, and then the appointee has to be approved by the European Parliament. This is not democracy as we know it, but appointment based on political elites and political lobbying.
The reason that Barroso opposes Scottish independence is because in the event of a Yes vote, the remainder of what is the United Kingdom will re-negotiate its position with the European Union. This will mean re-negotiation of the contribution that the United Kingdom gives to the European Union Budget, which in 2009 was 3.8 billion Euros. The United Kingdom is one of the fourth biggest contributors to this budget, a vast amount of funding which would radically change the economic and political structure of the European Union, if it were to decrease.
And that is why Barroso opposes independence. It is all about cash.