It largely depends on how it's handled, specifically whether the late character has been introduced early in the plot and simply joins you late in the story (Magus from CT) and whether the game utilizes a time consuming customization system and how the game compensates for the tardy party member.

Basically if the latecomer shows up late in the story, then they will probably be ignored by the player who has more emotionally invested in the characters who have been around longer. The only way to get around this is by either having the character just have a truly demanding personality that is easy to flesh out and hard to ignore or to simply have the character introduced in the plot earlier so they can be fleshed out even though they haven't actually joined.

Game mechanics-wise, it depends on how complicated and time consuming building characters can be. One of the reasons why many of the story characters are trout upon by players in FFTactics for example is that they start off far behind the characters you've been building and while they can be pretty broken in their own right, some players don't really want to spend the time to build them up. It's why latecomers or "secret" characters tend to have simpler builds offset with better stats or abilities.