One of the examples that pops into my head is Legion in Mass Effect 2.

Everyone levels up at the same rate, and Legion's a fairly versatile tech/tank, so in terms of gameplay Legion's totally usable. But, in terms of character development, Legion does get pretty short-changed, and he appears well over three quarters of the way through, so you can't really use him (for the main story at least) for that long.

Legion did get a very important role in Mass Effect 3 - although he wasn't playable - mind you, so at least they tried to make up for it.