Here is what I'd like to see, in order of PH chapters:
1) Above all, modify the rules to fit dragonlance, don't modify dragonlance to fit the rules. For example, sorcerers don't really fit in a 4th age campaign, orcs (and thus half-orcs) don't exist, and bards would have to be modified to use divine magic as followers or Branchala (and perhaps Gilean and Hiddukel).
2) Make all the common character races in DL available. For powerful races, such as Irda, Half-Ogres, Minotaurs, and Centaurs, create variants that are at most ECL +2 or +3, so they can be included in low and medium level parties without unbalancing the game. The minotaurs and centaurs of Krynn are simply not the minotaurs and centaurs of the monster manual. They're not as strong or as naturally tough (ie. don't have lots of natural hit dice). Krynnish Minotaurs and Half-Ogres are not even necessarily Large sized, just on the top end of Medium at 7' to 7.5'.
3) Don't be afraid to create variants of core classes. For example, you could create a Mariner variant of the Fighter, who gives up proficiency in medium armor, heavy armor, and shields for 4 skill points/level and having Balance, Intuit Direction, Profession, and Use Rope as class skills. Other appropriate variants might be a Handler variant of the Rogue, who gives up sneak attack for other kender-appropriate bonuses, a Ranger variant that doesn't cast spells (for characters like Tanis and Riverwind), and a divine Bard variant. A non-combatant version of the Cleric might also be appropriate.
4) Only use prestige classes when neccessary. For example, there's really no difference between Crown Knights and Fighters aside from roleplaying differences, but Sword and Rose knights have legitimate game-mechanics differences that warrant prestige classes. Similarly, Wizards of High Sorcery don't have to be a prestige class either. Just alter the wizard class so a character can't take more than 3 levels of it without taking the Test (or going renegate), and create rules for the fluctuation of magic power by the phases of the moons.
5) Include detailed gaming-relevant info on all the regions of Ansalon, as the Forgotten Realms book does, and include info on daily life. So far, the only parts of ansalon that have been flushed out are the places that the Companions spent time at. There are entire nations and cities that so far have little more than a name.
6) You probably have to include the fifth age, but definitely make the focus on the 4th age, with variations for the other time periods. It's quite simply the most popular time period there is. 5th age was a failure that alienated most core Dragonlance fans, yours-truly included.
Hopefully the concludion of the War of the Souls will solve the 5th age problem, and turn Dragonalnce back into the Dragonlance we all know and love.