Some of the rule changes have been safety driven as the cars became dangerously quick for the circuits eg. more restrictive rear wing geometry, extra wheel tethers, cockpit side protection panels etc
Some of the rules changes have been for cost and to keep it to a reasonable amount of teams. It was becoming an arms race where even spending $1 billion would be no guarantee of success so manufacturers started to leave. eg cost capping, multiple race engine/gearbox life, single tyre manufacturer etc
Some of the rules changes have been to keep the competition tightly bunched as this year with many different drivers on the podium and a championship that will go down to the wire. eg tyres again, limit on windtunnel time, limit on testing, restricting innovative new solutions
Some of the rules have been to embrace a green future, these for me are BS but necessary eg KERS, 2014 small capacity engine with restircted fuel flow
Some of the rules have been changed to add more excitement, these have probably been the least thought. Some very bright minds have spent a lot of time coming up with them which should give an idea of how hard it is to get right eg DRS, no fuel pitstops
Almost forgot, at least one rule changed because I was good at my job, sorry
what happens in Vegas stays in Vegas
Most of the technical rule changes are discussed by the teams and then proposed to the FIA, the FIA set the rules and these changes effect the excitement of the racing much more than any effect Bernie has. Sure he will be behind the scene's lobbying and sorting out deals.
I have to agree with a lot of what's been said, the above are not excuses, just a few observations of how F1 has changed while I've been 'involved' in it from 1996 until now.
As for the new 2014 1.6ltr V6 turbo era don't expect F1 to go back to the glory days of the 80's