I think it really depends on the game. The biggest problem I have with characters that arrive late is that they are always lagging behind in terms of learning skills and abilities, which often makes them more trouble then they are worth. Should all things be equal then I don't think I am that biased against them, just going from examples in this thread I use Emerelda, Eiko and Amerant as my mains.

I do think the are easier to forget about from a story point of view, being around for a shorter period of time means they have less memorable moments.