I don't really mind when the idea fits and its fun, I don't even mind that companies divert resources into making them -- they gotta do what makes them money. It's only really when it steers well loved franchises or game ideas away from better suited hardware that it becomes irksome.
I'm willing to be turned around on them, but Layton 7 for example... Breath of Fire 6... I dunno. In the case of that new game in the Layton universe it looks like such a massive departure that you can't really know how to feel. The traditional puzzle adventure games would probably work fine on a mobile, I don't get what they're trying to do there.
Anyway, I didn't realise Atlus were sort of in deep with mobile games already in Japan --
if SEGA can help steer them to greater success and more localisations, this is probably a good thing. Remains to be seen though, doesn't it.