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I dont like the way kmail2 makes directories for incoming emails for imap account.

I have 4 pop3 email in incoming/ local folders, folder in kmail. Each of them have own folder, where kmail keeps messages.

But when I added a new imap account, I got seperated folder for those messages
on the bottom of the list.

I think that imap messages should have their dir also in local folders in incoming in "special" folder for it exemply with the name of that account
like on this picture
[img]http://farm8.staticflickr.com/7161/6476614065_9ec66c287b_b.jpg[/img]
http://www.flickr.com/photos/69767255@N06/6476614065/sizes/l/in/photostream/

Many people are indeed confused at first by the way ressources are handled in different ways.
But we have to keep in mind that mail boxes filled via the pop3 protocol and imap4 ressources are something very different. It is not just 'how' the messages are downloaded to your system.

Technically your "pop3 folders" are not even accounts, but simply local folders in the file system where messages are somehow dumped into. Might be via pop3, might be something completely else, like fetchmail, rsync, nntp, ... The is why the collection is called "local folders".
Imap4 works different. Usually the messages are not even stored locally, except now in the akonadi cache. Instead the idea behind imap4 is that you access data n a remote system via the protocol. Data not only being email messages but also addresses, notes and calendars. I doubt is would be wise to copy all those things to every system. This is not the idea behind the protocol.

On the other hand I do agree with you, that technical differences must not neccessarily be visualized as is.