CCP Ytterbium has gone on the record to say that there are changes coming to the factional warfare system. While the entire system can't be completely cleaned up in one go, Ytterbium has laid out a series of modifications to make the system more lucrative and playable.
For instance, loyalty points (LP) are finally being given out to gangs of players who kill other players involved in factional warfare. These points can be spent in the faction navy loyalty points store for the usual items, except all of the "usual items" are undergoing some nice price cuts if you're involved in factional warfare at the time of the purchase. In addition, a brand new set of items exclusive to factional warfare will be added into the LP stores to provide even more incentive.
Also of note, the hit points of control bunkers, the proverbial "capture points" of star systems, will be increased to make them more durable. While CCP doesn't want these bunkers getting to be on part with starbase control towers and encourage huge masses of ships "blobbing" targets, they do want factions to be able to muster a defense before a control bunker is lost.
For the full run down of all of the changes and additions, check out Ytterbium's post on EVE's website.