I've thought about this quite a bit. I think that if I were in a position to write some or all of a sequel's script then I'd put Ramza with Rafa (now older) for a list of reasons and have Agrias fall into the arms of comforting, understanding, protective, courageous-yet-quiet Mustadio after losing her beloved Ovelia. She is a bold Type-A, he is quiet Type-B, and yet they still have a lot in common- I've seen many great matches like this in real life. I'd put Alma with Olan - it would explain a lot of stuff and also act as great plot fodder in a sequel. I'd place Meliadoul with Alma after Olan dies at the stake for the sheer drama of it.
There's a lot of potential, here. I enjoy the speculation.
This is my version of Final Fantasy Tactics. I've been tinkering with it for a few years, now. It is based upon vanilla PSX Final Fantasy Tactics. By this point, all monsters, jobs, items, abilities, and encounters up to chapter 3 have been changed. Many mechanics have also been changed. I have finished all encounters but the chapter 3 and 4 story battles- I'm hoping for a bit of feedback before I dive into that.
Just use PPF-o-Matic or a similar program to patch your vanilla FFT .bin file.
This modification is possible because of the tools I have discovered at ffhacktics.com . I did not code the ASM hacks. I downloaded from the above site a Patcher program to modify the game, a text editor to edit in-game descriptions, and the ASM hacks. I created the redesign of the game alone using those tools.
The game is now based upon 'tactical diversity of threat' rather than 'upgrades'.
Jobs: All normal jobs are balanced with each other and are freely available.
All jobs are highly customized. 'Select' gives detailed information on each one.
Bard and Dancer are now mechanically the same.
Stats: Statistics are now based upon job history, equipment, and gender [I haven't figure out how to remove gender]. The current job now does not affect stats- work history now covers that. Growth rates are based upon a 'high/medium/low' system and are listed for each job when selected.
Every ability has been changed. Abilities are now balanced with each other and priced accordingly. Jobs are now meant to be more fluid. 'Spellsword' is a viable archetype, now.
The magic system is now based on tactical diversity rather than upgrades. Instead of 'Fire 1, Fire 2, Fire 3, and Fire 4' there is now 'Fast Fire, Far Fire, Wide Fire, and Strong Fire'. Magic and physical abilities are meant to be balanced and synergistic.
The item system of the entire game has been changed. Every city with 'Trade' in its name will have all chapter-appropriate items for sale- but you might not like the price! Stealing and poaching are now very cost-effective, but no longer will you have to spend a long time in side quests for 1 item- all items are replaceable, but the gil cost may be high. Items are more important when it comes to stats, and all weapons are now based upon PA. Weapons and armors have other niches to fill, now, instead
-random unit equipment more selective
-crystals can include special job abilities
-all formulas apply elemental
-require materia blade -> require knightsword 
-Weapon XA Rewrite.
Formula = 34 for all weapons but Fist
Fist = A0
Stat = 24
Const = 3
-Units rot or reanimate without skipped turns
-level down based on historic growths
-broken/stolen items can be bought back at fur shop
-AI attack transparent unit
-special characters can do propositions
-Job X is mountable. X = 88 [dragon]
-No monster breeding
-Soldier office can rename any units
-Cannot Hire Soldiers [use Invite, instead]
-Secret Hunt Not Needed To Enter Fur Shop
-Undead units ignore phoenix down
-undead units recieve 0 damage from healing ability