Its more a case of making a theme fit the current play style.

A lot of people complain about summoner. In the older final fantasy games summoners would just do a big attack and that's what a lot of people want. Would that really work in the game though? Everyone running around keeping their buffs up while summoners press a button and watch an attack play out? I think Dreadwyrm Trance was a good way of portraying that, charge up your aether then perform a big powerful attack.

I like the idea of DoTs on a summoner because they do something that most attacks can not- allow you to deal damage while concentrating on other things. A way it could be fixed is by keeping dots, and when they are applied, do some abilities that affect the way your pets act. My ideal summoner in 4.0 would be one egi that replaces all the current ones and gives you someone to do in between trances other than spamming ruin. That would feel a bit more summoner-y.

As for ninja, I think someone has already said that but stealth isn't easy to implement in a fast-paced game either. I just can't think of how you wold implement stealth mechanics.