Darrell, are you saying the removal of Magic EXP is a pro or a con? Hard to tell.
I guess I'll give this a try, though it will almost certainly be quite incomplete due to minor things that aren't as fresh in my mind like the details of different monsters. A lot of things will be repeats of what Darrell said, with a few disagreements and additions.
SSS Pros:
+ Character portraits added a lot of humor
+ More dialogue to flesh out character and storyline
+ More sophisticated magic menu, showing what and how much each spell did instead of needing to guess like in TSS; ditto with other items and so on
+ More sophisticated "range" instead of "moves" prevented zigzagging around on the battlefield (although, as with many SSS changes, this actually originated in EB)
+ Nash has a few non-thunder spells (though not much use regardless)
+ Phacia (not so enthused about Royce, though)
+ Secret items to find, such as bromides, Ghaleon's Tear, etc
+ More Luna time to establish her as a character
+ Better sprites, though still room for improvement
+ Some nice cutscenes, though really only the Dark Goddess stands out to me (because of the music)
+ Ghaleon playing the lute, and other fleshing-out of his background with Dyne
+ Brief epilogue in Meribia to wrap up loose storyline ends (and show Laike and Mel satisfyingly de-stoned)
+ Some dungeons fleshed out and made more complex, such as the dragon caves
+ Nall revives
? Visible enemies less aggravating when you want to level up, but made the world kind of empty
? The Frontier explicitly the dark side of the "moon". I haven't decided how I feel about this one.
? More music...although TSS got along just fine with the smaller quantity of pieces
SSS cons:
- Music made more generic in both complexity and sounds, sometimes downright dopey (Lyton/Blue Dragon Cave), and the single most boring and even ugly piece of Lunar music included from EB (the thud-thud-thud cave music)
- Gaping plothole introduced in that Quark/Luna capture scene
- Less interesting Mel's Mansion
- Nash changed from a loyal, clever double agent into a cowardly traitor
- Ghaleon's character weakened as noted earlier, and also Althena's "retirement" lessening the impact of her staying with Alex
- Cool, austere, mysterious temples of Althena turned into pseudo-Christian cathedral complete with organ and stained glass -- another carryover from EB, but thereby weakening the effect of the change between TSS and EB
- Way too few spells, and of very predictable types: attack one/some/all and support, a stripped-down version of EB's without the interesting changes (on the other hand, some might argue that having the different dragon spells do different things is more interesting); no healing spell for Mia or Alex until the overpriced Dragon Healing
- Smaller and less interesting world map; since there are no battles on it, there's no reason for anything but the main locations to be on the map and thus nothing much to explore
- Can't easily run any more, making levelling up more tedious
- Spoiler in Ocarina song list
- Ocarina instead of harp (possibly related to Ghaleon playing the lute)
- Battle voices, and more voices in general... I know, I'm the only one who thinks adding these was a step back
- Kyle ridiculously slow, considering he's a professional fighter; Nash ridiculously useless instead of being a half-decent fighter
? Royce -- too much a clone of Xenobia to be terribly interesting, and therefore pares Xenobia's appearences down so much as to make her negligible
? Remake COULD'VE added a Fresca/Mia/Jess dungeon to balance the boys' club Black Dragon Shrine, but didn't -- bah!
? Fewer, if any, hidden chests?
Legend pros:
+ Better sprites than any other game in the series, especially the charming battle animations
+ Luna uses a frying pan, which is rather funny if ridiculously sexist
+ Cards are fun to collect
+ Some hidden or hard to find red chests and a couple other secrets, like the Protector's Cave and the red chest in Ramus's shop whose contents change depending on when you open it
+ Special equipment sets are kind of fun
+ Arts gauge moves aren't necessary, but again are kind of fun (if balance-wrecking)
+ Alternate storyline bits at the beginning taken from first novel and drama CD, including interesting examination of becoming a dragonmaster
Legend cons - almost all of the SSS ones plus:
- Lousy AI for battle tactics -- that is, there is none; the targetting is apparently random
- Music quality
- Balance issues, such as the overpowered Meteo Rod
- One-time-only dungeons
- Battle... actually, just about all of the cons that are Legend-specific are directly related to it being on a handheld and just not having the speakers or screen real estate to do things like the classic battle system or explorable overworld map. And, of course, additional cons from the rushed localization. So I think I won't bother going into further detail there. For the most part, I'm OK with the tradeoff of really nice sprites in battle in exchange for dealing with a random, range-less battle system (which does at least have zone attacks and some variation in DEF depending on location).
EBC pros:
+ Character sprites
+ Hiro not being such a jerk
+ Ruby marginally less irritating
+ Funnier opening with Hiro running from the Inferno Ghouls
+ More epilogue dungeons
+ Bromides
+ Easier to steer Destiny
+ A few small subplots, like the Nota group and the person lost in Zulan
+ Possible to see Lucia's spells and stats under some circumstances, for people who like numbers
+ Fleshed out backstory for Jean and to a lesser extent Ronfar and Mauri
+ Flashback of Althena being her actual self, not just a retired goddess or a picture
+ Crest system interesting, if overdone (I probably wouldn't take it over the loss of M Exp, though)
+ Some fun items and accessories, like the pajamas
+ Complex Zophar battle (I haven't played the original in a while, though, so can't compare easily... I'm just thinking of all the extra arms)
+ Some fun battle voices -- well, some fun running-away voices, like Ronfar's Gambler quote
EBC cons:
- Less interesting and complex dungeons by far
- Too many Lucia bathing scenes, and rather forced ones at that
- Azado butchering, also as noted earlier
- M Exp removed... I really liked that, and didn't mind the paying for saves either
- Tying all magic to levelling up meant that spells morphed into more expensive ones unavoidably
- Some spells less interesting, like Ronfar's Chance Dice
- Despite five separate elements, many enemies vulnerable to all elemental magic (as opposed to direct attacks or non-elemental skills) more or less equally rather than weak to some and strong to others
- Still single-combat battle at end, so no real use for all that levelling up and cool epilogue items found for others (not really a change, but should have been)
- Simplified world map, though perhaps not as much as with SSS
- Overpowered spells, e.g. Triple Sword
- Red Dragon Anger (and Black Dragon Grief?) still useless
- More boring and easy boss battles
I guess that's about it that I can think of offhand. I actually like all of the five games mentioned, but still have a preference for TSS and a growing appreciation for EB, which I think may be the best overall game even if not my favorite. I've generally tried to avoid mentioning things that are localization-specific, with the exception of the few voices I mentioned.