First off, let it be known that After Effects is used in feature film work all the time. I’m sure many here will be able to concur.
Now, coming from an experienced AE user, who has begun to get his feet wet with the node based compositor NUKE, all I can say this…
In large, complex comps, node based workflows are much more organized. Honestly, I think that is really the biggest difference. As you may already know, using AE, it is too easy to get lost in multiple nested pre-comps and hundreds of layers taking up your workspace. Node based workflows avoid these issues, and make it very easy to pass off the project to other members of your team. Aside from this, compositing is still compositing, and both apps can produce the same results.
But because AE is so widely used, and has so many great third party add-ons, I think it is still extremely valuable to know and use. Particularly on projects that are not hundrerds of layers or need to be passed off to someone else.