This question is a bit tricky, because while I do agree that Heracross and Donphan are strong that not neccersarily makes the others weak. Or bad handled, because when Ash has as many Pokémon as he has, the writers can´t give them all the same attention. And I mean, when one plays a NDS game, then you usually field a lot fewer Pokémon than Ash ever does (I uses 4 high level Pokémon to take out the E4, and the two remaining spots are taken by pretty low- level Pokémon, Ash could probably field 2 DIFFERENT full teams that are pretty even in strength).
Heracross is definitly one of Ash overall best Pokémon, and would be put in many dream team line- ups (just check that thread). Then we have Donphan that are strong, and if Ash battles right, can do lot of raw power damage. But he can also be swept of the field pretty easily. Quilava is probably strong but has Infernape and Charizard as main competition when it comes to fire- power, and that it his loss. I think that, given that all fire- types are avalible, Ash would RIGHTLEY favor Charizard and Infernape and then Quilava and Torkol would have to take the back seat. Between them I think it is pretty even in power. And he did use both in the Sinnoh League.
Bayleef is a good supplement to Sceptile now when Torterra just isn´t the right kind of Pokémon for Ash, as the Sinnoh League clearly showed. So I won´t agree that she is handeld badly at all, on the contrary.
Noctowl is great when he neds such a Pokémon but when it comes bird both Staraptor and Swellow is better, that´s just how it is. Totodile is probably the really weak one and the only one that might be handled badly, but then Ash is not much of a water- Pokémon trainer and Buizel are clearly his first choice now in Aquirtles abcense.
So overall I don´t think the team is badly handled, they actually has a lot going for them. Heracross is one of Ash best Pokémon and Bayleef would be the perfect supplement to Sceptile.