Well, upto gen 3, i don't really think there was any problem with genders. The trouble starts in the 4th gen. Frolass (Snorunt's alternate evolved form) is a female only species. That kinda makes Glalie it's make counterpart, but Glalie can in fact be make OR female. Similarly with Gallade/Gardevoir.
The only one gender based restriction which really makes sense, is Vespiqueen. Combee only evolves if it's a female, which is true, only female bees can become queen bees.
Also, kinda on topic, has anyone noticed? Cressalia, a female only species, had a genderless counterpart! Darkrai!