Okay, first off I would recommend adding some required proficiencies to the Unarmored Defense feats, Dodge and Mobility for the intermediate and advanced feats respectively, having had a PC with all three feats at first level almost soured me on the feats, adding the requirements slows them down just a tad. Other possible choices for requiremens include Lightning Reflexes, Tough, or Great Fortitude.
On the whole the classes balance against each other better than their 7th Sea equivalents, just not against straight D&D characters. (Well the feats more than anything else really)
I have implemented the 'Karma Dice' from the 7th Sea Gamemasters guide, changing the dice from d10s to d4s, in keeping with the lower rolls typical to d20. The first time a black d4 entered the pot you could see them get worried... When Alfredo fell from the roof and suffered both the damage from the fall and an ignoble defeat they were almost relieved to have it out of the pot. I have found Karma dice the best way to reward heroism and punish villainy/stupidity. The party started policing themselves very quickly.
I would also suggest having the more prestigious of the Swordsman's Schools requiring a mentor, or even a blackball system. (All the assembled leaders of the guild placing either a black or a white ball into a black velvet bag. If even one ball is black then the answer is 'no', the player can't join the school that season. (Finding out who cast the blackball and why can be an adventure in and of itself.)
Membership is a feat that needs some tweaking, the fact that it basically tosses the ball into the DM's court bothers me a little, some type of 'membership ranking' may be necessary, who can ask what of the secret society and at what rank. A simple level test with a charisma modifier may be the ticket, varying the DC with what is being requested. (5 for a night's lodging, 10 for being hidden from the City Watch, etc.)
The other part that needs work is Dracheneisen, I would recommend making a feat to be taken at level 1 that determines how much Dracheneisen the PC is in a position to inherit. Unlike 7th Sea I suggest NOT allowing the PC to begin with Dracheneisen. With the PC determining at what level the inheritance kicks in, the longer the wait, the better the armor. I have not yet come up with a chart that I feel happy with, but I am getting close.
I strongly suggest not choosing the 'you get nothing' option for the Faith feat, it just ssems completely unfair, both in d20 and 7th Sea.
I am still coming to grips with Swashbuckling Arcana, the magic is so much more versatile than in 7th Sea, while being in some ways strangely vague, lots of 'flavor text' suggestions.
Some of the added flexibility I agree with, the ability of Glamour mages to cast illusions make perfect sense. The spell casting abilities of Porte mages is a little less understandable. Necessary to balance the Sorcerer classes against each other, but somehow a bit flat. Frankly I was expecting a feats based system, allowing the sorcerous abilities to be taken while the PC remains in another class, oh well.
A hubris not in the game but highly recommended is 'Evil Twin', yeah, it’s a cliche but boy it can be fun, as is 'Inconvenient Friend/ Relative' who always shows up at exactly the wrong time, and 'Embarrassing Twin', not evil, not misunderstood, just feckless and foolish.
If you are running a sea based game make sure the PCs get a map of the ship, and a chance to customize her and make her their own. (There is a nifty free program for mapping called Dungeoncrafter, one of the user submitted sets for the program is for mapping ships. Handing the PCs a map of the ship really helped them get attached to her.
Http://www.Dungeoncrafter.com for the program itself,
http://underworld.dfxwebs.com/dc1customs/ship.shtml
for the ship tileset.
I would also change the guns to martial weapons, the flintlock has been invented in Thea, and guns are very common.
Non-rules advice follows, feel free to ignore if you already feel up to the game:
Start with a bang, I began my most recent campaign with a mass battle scene, with the PCs pinned in the cellar of a collapsed building by artillery fire.
Try to get the players to design a party, not just individual characters. Give them some core to create their band of brothers around, be it ship, king, or organization.
Set up scenarios for SA as if they were scenes in a t.v. series, time breaks to coincide with cliffhangers, silly, but it works. Try to end each session except for the last one in a scenario with an action based cliffhanger, swinging from the chandelier, the thugs leaping off of a low roof onto the party, the closing vessel raising the Roger as she turns to broadside, etc..
Feel free to swipe story ideas from any action based game/movie/book, I did a game based on Sweeney Todd once, lots of fun when they went into the barbershop to meet their spy contact, only to find that he had 'disappeared'. (Care for a meat pie?)
For miniatures, I have been using a combination of plastic Games Workshop Mordheim and Empire figures and the Pirates of the Dragonspine Sea set by Reaper Miniatures. Reaper miniatures also makes a figure called Razig the Undead Pirate (Reaper Miniatures 2437), which is a scenario waiting to happen. I ended up using Mordheim accesories and plastic skeletons and zombies to give him a ghastly crew. I just used the rules for Wights from D&D and gave them pistols and cutlasses. For some reason the one carrying the lantern scared the PCs, so I gave them a reason to be scared... part of being a D.M. is knowing when to steal ideas from your players

. (It was fun afterwards listening to them congradulate themselves on the accuracy of their 'deductions'...)
Hmmm, went on a bit longer than intended. Good luck with the game,
The Auld Grump