There's actually a big difference between the two. If you're on a budget and don't mind that editing video is not as straight forward, then Motion is actually not a bad route to take.
Final Cut allows you to use things you've created in Motion as graphical templates. Motion in and of itself is a 2D(/3D) animation app, it wasn't made for video editing.
So, although you can edit video in Motion, doesn't mean it's very comfortable. For instance, you can just press a shortcut to render your timeline in Proxy, High Quality format. If you'd do the same thing in Motion, you would have to encode the material by yourself and tell Motion manually to use the Proxy's instead of the original material.
Final Cut also has some media management tools that allow you to quickly find the footage you want to edit. So if you imported tons of clips, it's easier to find a particular clip in FCP than in M5.
Both apps work well together, but in itself, Motion wasn't made to edit video. If you come from iWork. Editing in Final Cut Pro is almost equal (if not the same).
I can't talk about Avid, Premiere, but they work similarly to the "old" way of editing video, where the timeline is static. When there is a clip deleted between two clips, they don't ripple together. They stay at their current position. Some people prefer to edit that way. Personally I can't see myself going back to that way of editing, it is simply too slow.
Now in regards to 3D… Motion is a 2D motion graphics application. It can do 3D too, but it misses most features "real" 3D apps have like fluid or explosion calculations of material. Material can also have a real material. So the app knows that wood explodes differently from glass. If you are new in 3D animation and just want to tip your toes in, go for Blender. It is hard to learn, though, because it's free, there are tons of tutorials available online to get you quick up and running.
After Effects is the industry leader in motion graphics. It is said that nothing can't be done in After Effects. Motion tries to an After Effects. It is also said that Motion can do everything that After Effects can, but, again, with more effort.
As a summary. If you're on a budget and need a great 2D motion graphics app, Motion is not a bad choice. It works well together with Final Cut Pro, a video editing app that is similar to iMovie. Though 3D animation can be done in Motion, it is better to use a dedicated 3D animation app like Blender. If you really want the most top-notch effects, templates and biggest community (and can afford the price of a monthly/yearly Cloud membership) go with Adobe.
Hope this helps.
