I'm gonna try to keep this as spoiler free as possible. I haven't gonna far in the main quest yet, but it seems like its going the direction of *spoiler* Dragonborn trying kill Alduin to stop him from resurrecting dragons *spoiler* Now my question is will I be able to harvest dragon souls and have random encounter with them, after I finish the main quest?

Thanks,

Yes

yeah, dragons will still be there even after you finish the MQ

Thanks.

Of course you can:)
Its not like oblivion when every oblivion gate dissapeared

It seems implausible though, even though true. I mean after the main quests, the dragons (all of them probably) know what the Dragonborn is capable of right? So is it rational for the to keep trying to ambush him from the air? How stupid do the dragons have to be to not run for their lives when they see the Dragonborn (in dragonbone armor no less)? They do keep attacking you though, pathetic though they are.

(spoilers) Odhaviing (sp?) mentions that many dragons have begun to question if Alduin really was as powerful as before, and Esbern says that they are prideful by nature. So it could be that they are simply trying to become the next leader.