It's a game and so ultimately recreational, therefore I fail to see why any player ought to be penalised on his choice of alliance because there's a minority of the player base that dedicate exuberant amounts of time to the game in order to play it competitively. This is something you will find in all games, and I think people need to get it out of their heads that being the top alliance or one of the top twenty players is the be all or end all to the game.
There are enough competitive players that the "winning" group will not always be the same ones, and so, I don't feel that it's a problem that we need to remedy in and of itself. Making alliances a random affair is really not the way forward to solving this supposed problem.
It generally comes down to people that are playing it leisurely, and while contributing a fair amount of time to the game, they are not playing it actively enough to be considered "in the running", shall we say, and so the consensus is that the game is ridiculous unfair and imbalanced.
I would suggest, if you genuinely want to address the issue, that you consider alternate ways for people to accumulate some manner of recognition or purpose to their play. Obviously this is something Azzer realized a long time ago, hence the introduction of Bounty hunting and Honour/Fame etc that we've all seen before. That's the direction you need to expand in should you wish to cater to the more casual gamer.
Hardcore groups are always going to play for the win and it's not for you or I to punish them for that. You get out what you put in, as they say.