You're really asking two separate questions here.
1. Won't there always be a best deck?
Yes, there will. But there are two key considerations that also tend to determine how much people complain about that deck. The first is how big the gap is to the next best decks; if there are a range of viable alternatives to the best deck, and in particular if those decks have broadly different strategies and attack the opponent in a variety of ways, then hey, you've got a healthy meta game. As an example, while Foodcoats was at it's strongest Fastrobiotics was also a very strong deck choice that played in a totally different way.
The second part to that question is simply whether the games against the best deck are fun or not. Foodcoats tended to produce quite close, strategic and exciting games of Netrunner. Hot Tubs and IG54? Not so much.
The reason (and I realise that you didn't ask this question) that so many people are begging for an MWL update right now is that both of these factors are negative; there aren't enough alternatives to the best decks, and the games that those best decks produce are often not very fun.
2. Shouldn't the MWL target broken cards instead of powerful decks?
Who knows, frankly. One of the issues that Netrunner is dealing with right now is that nobody, least of all the design team, knows what the MWL is actually for. We can extrapolate reasons based on what Damon said when it was introduced and what cards have been placed on it, but it's still far from clear. Is it designed to reinforce the colour pie (hence Lady's inclusion?). Was it to help expand design space (Pre-paid Voice Pad?). Was it to encourage diversity in deck building (Desperado?) or tournament representation (Wyldside?).
The truth is that it's been used as a hodge podge of all of the above, which means that the strategy of what cards should be added to it (and at what levels) isn't particularly clear. One of the things that I'd like to see under Boggsy's reign is that they clarify what the MWL is trying to accomplish, and if it's a balanced tournament meta game then it should be handed over to the OP department to maintain rather than design.