I agree with FlyPNS1's concern of forcing airlines to serve specific types of markets, but something is needed to ensure adequate access to both low-fare and traditional carriers to the slots that would open up.
Also, control of these slots should be a local issue, not a Federal one -- let the market steer itself, rather than be told where its routes should go (which smacks of CAB regulation).
Maybe something along these lines (bear with me, it's long):
Appoint local advisory councils to determine the mix of traffic that is needed at LGA and DCA, including representatives from local airport/port authorities, government, business leaders, community leaders. Do NOT include airline executives or representatives on these panels.
Once the benchmarks are determined, publish them and open a Call for Proposals to the airline community. Receive sealed 'bids' for service and have the same advisory council review them.
Allocate slots based on Calls for Proposals and open negotiation with carriers to enter into an agreement for service. The agreement would grant slots for use on specific routes (outlined in the Calls for Proposals), set targets on performance, set targets on total end-user cost (including fees), and set targets on customer service.
Agreements last for one year. They are renewed or terminated according to terms in the agreement. For instance, if an airline exceeds average end-user cost targets by 20%, then their slot charges also rise 20% for the following year. If an airline beats the end-user cost target by 20%, then their slot charges fall 20% for the following year.
If an airline exceeds the target end-user cost by a large amount (50% or so), their agreement is terminated and the slots go up for grabs in the same process.
The same system is used for other benchmarks: customer satisfaction, on-time performance, security, etc.
Also, slots are bound to particular routes and frequencies -- airlines couldn't reduce frequencies or change destinations midway through the year. At the end of the year, they could renegotiate with the local board to get service changed.
Finally, airlines would be prohibited from predatory actions against other airlines on routes served to or from that particular airport, regardless of whether they're covered by the agreement or not. For instance, at DCA, Frontier already flies DCA-DEN and wouldn't be under this agreement. If United comes in and wins a DCA-DEN route under this agreement, and then gets predatory on ANY route from DCA, their right to DCA-DEN is revoked.
Long, I know, and definitely a pipe dream, but I think this would be an ideal way to control slot regulation -- communities get a direct say in what they want, what they're willing to pay for it, and then airlines can bid for what they want to serve and at what price targets. If a price target is too low, then a community has to either decide to pay more or change their desired routes.
There's enforcability, incentives for low fares, and a way for either side to get out of the agreement after the year if market conditions change.
Just my $0.02...