Dude, leaving rinoa out is mean:P

Have three sets of junctions, yes, but keep one of them permanent and assign levels to the others.

Like Squall has certain junctions, and in the segments he's not in battle, have someone, say Irvine, be the primary junction accepter (think photosynthesis here) and if Irvine is already in the party as a higher up level for someone, have a secondary junction character, like Rinoa. Zell might be person number three, followed by Quistis then Selphie.

Then you more or less separate the other two sets of junctions in 'mostly the ones that Quistis uses, Selphie and then Irvine then Zell then Rinoa will use these' and 'mostly the ones that aren't used, give them to Zell or Rinoa, and then Irvine, Selphie, and Quistis.'

Like this, if Squall was in the party, he'd get his GFs. Then if it was Irvine and Rinoa, Irvine would get set number 2 because he's closest to the front, and Rinoa would get set 3 for the same reason.

If Squall isn't in the party and it's Zell, Selphie and Quistis, Zell would get set #1 (squall's set), Selphie would get set #3, and Quistis set #2.

It's a lot more confusing, so I just think of it as 'oh, this junctioning has queza, I'll give it to irvine since quistis and selphie aren't here.' 'Oh, squall isn't here, but I've got zell, so he gets the set with shiva'

Anyways, towards the end of the game, it's smart to keep as many GFs with the different statjunctions as possible evenly spread. And because I've used about five million(or three) index cards to figure this out, I shall share

Assuming: All GFs available, all stat junctions learned, none of them erased, none added. This also fits the compatibilities and associations I've given to the characters and GFs, so it may not fit your party as well

Set 1) Shiva, Diablos, Pandemona, Cactuar: redundancies: [1], in STR junction.

Set 2) Quezacotl, Cerberus,

Set 3) Carbuncle, Eden, Brothers

There is some maneuverability in this, but NEVER put Shiva, Quezacotl, and Carbuncle together. With the normal abilities, they are the ONLY ones that can junction to Vitality, which is very important, especially because Meltdown is so useless everywhere else. Speed is less of an issue, but still, you should separate Pandemona, Cerberus, and Eden as well, Hit is less of an issue because that can be maxed on two different weapons (selphie's strange vision and all of squall's) but just keep Diablos away from Cerberus and Eden if you can.
Doomtrain, Bahamut and Tonberry are more or less moot, because they don't allow for stat junctioning unless you feed them a new ability, so put them on whomever you will. Remember that Doomtrain has status and elemental x4 defense junctions, so try to avoid pairing him with Alexander and Cerberus.

Obviously I didn't use nearly all of the GFs by any stretch of the imagination. Set one allows for an increase in *EVERY* stat (not including the elm and sta atks and defs), set two lacks EVA and LUCK, and set three lacks LUCK. Ifrit, Siren, Leviathon, Alexander, Doomtrain, Bahamut, and Tonberry can be assigned at will. Separate Siren and Doomtrain, for more status defence and attack, Ifrit, and Leviathon can go with anyone since the three sets already have one elemental GF each (except maybe brothers. I think they're elemental anyways) and give Alexander to someone that doesn't have Doomtrain. If you're levelling up, give Bahamut to the person with cactuar, obviously

the way I would have them assigned in the level importance I mentioned at the beginning would be:

Set 1) Squall<-primary. {Irvine, Rinoa Quistis, Selphie, Zell}
Set 2) Quistis<-primary. {Selphie, Irvine, Zell, Rinoa, Squall}
Set 3) Zell<-primary. {Rinoa, Irvine, Selphie, Quistis, Squall}

Realistically, there are ten main groups that your party can be in (excluding missile base and ultimecia's castle and possibly somewhere else.) I find the above to be satisfactory with all except like, four. Which mostly consists of characters I don't use a lot (quistis and zell)

Um, yeah. I think this was mostly useless, but I had to use those index cards for *Something* ^_^

Oh, and malboros are awesome. Equip someone with Devour and use demi about a million times to get spr+ (they have drawable demi, so as long as you can keep confuse and berserk free, you're good to go)

*out of wisdom*