Was it for the simple reason that London was a more important city, and England a larger, more populous kingdom, or were there other political considerations (such as assuring English nobility that he didn't intend England to be a Scottish vassal)? Was consideration ever given to ruling both kingdoms from Scotland? Was there Scotch push back to the move, considering the centuries of animosity?
The main reasons were that England was richer and that James enjoyed London more, both due to the riches and the comparative lack of Reformed influence. It was completely a personal decision on James's part, though someone could definitely attempt to justify it on economic grounds.
The Scots were definitely dissatisfied with this. In fact, when James first went south to England, he promised to return to Scotland at least once every three years - but he never returned at all.