Secret Characters: This point applies to all of the games, so I'll go over them all. The special characters are great. Unique jobs, unique sprites, great personalities, and fun missions to unlock them. But they aren't perfect.
First, limited story after they join you. With these awesome characters, it's a shame that they never show up in any of the plot scenes after the join you. For some of them, they join so late that it doesn't matter, but I would like to see at least small appearances in the stories after they join up. Take Frimelda. When your clan is sitting around the cities after the missions, she should be there if you have her, and get a couple lines. Same thing with Ezel in FFTA (others aren't availible until after you beat the game in that one).
Second, let them join at low levels. You usually don't get these guys until late in the game, and picking them up at too high a level to stat train means that they tend to be weaker than the rest of your team.