The 3rd round should be seeded so that the Minnows get their big match.
90 mins then penalties..
I wouldn't do that because you play into the hands of the big clubs. What I would suggest is that, at the time of the draw, the home team is the one which is lower in the league pyramid. Agree with the 90mins and penalties though. Of course, smaller clubs would lose out on the big payday at old Trafford etc but would give them a better chance of progress.
Failing that, the only other way to improve the cup is to give the winner one our our Champions League places but I can't see the Premier League agreeing to that!