Both can put two proficiency points in a weapon slot, but the Swashbuckler doesn't get the extra 1/2 attack per round for the second proficiency point. I don't think it should be that way, but that's the way it is.
I think that Fighter/Thieves get more proficiency points than Swashbucklers. Swashbucklers start with four at 8th Level and receive one additional proficiency point for every four additional levels. A Fighter/Thief starts out with 6 proficiency points at 6th/7th Level. Level for level, Fighter/Thieves get more proficiency points than Swashbucklers, but single-class characters advance much faster than mult-class characters.
Swashbucklers and Fighter/Thieves can both put a third proficiency point in Two Weapon Style.
Fighter/Thieves can put two proficiency points in bows (long or short) and missile weapons. Swashbucklers can't. (I can't resist pointing out that throwing daggers are my favorite "missile" weapons.)
Swashbucklers can't backstab.
Swashbucklers can have Whirlwind Attack, but Fighter/Thieves can also have it, as well as Assassination, Greater Whirlwind Attack, Power Attck, Critical Strike, Death Blow, Greater Deathblow, Hardiness, etc.
I'm not sure which one has a better THAC0. A Fighter/Thief starts out with a better THAC0 (you can backstab effectively at 6th/7th Level), but a Swashbuckler advances more rapidly and gets bonuses, so I'm not sure how it works out at equal levels of experience (which translates to time spent playing the game).
A Fighter/Thief can have STR in excess of 18 ("18/01-18/100), and a better CON bonus if your character's CON is over 16. (Elves are limited to 17 when you roll one up.)
If you want to play an elf, remember that they can have a DEX of 19 when you roll one up, and they get a +1 bonus with longswords and longbows. Roleplaying issues aside, a Fighter/Thief can backstab with a longsword, and personally I don't see any problem with it.
Personally, I tend to play dual-classed humans more than anything else. A Fighter dualled to a Thief is great (or a Kensai dualled to a Thief, or a Berserker dualled to a Thief). So is a Swashbuckler dualled to a Fighter, or even a Cleric. (Gotta love Use Any Item.)
If I had to choose between an elven Swashbuckler or an elven Fighter/Thief, I'd probably choose the Fighter/Thief, but actually, I've played both (very similar characters, anyway).