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I am wondering how to best connect Android smartphones with Linux boxes.
The best thing would be a program like Samsung's Kies, but Samsung seems to target Windows and Mac OS.
Is there such an application like Kies that runs on linux natively (not wine), so the user can connect Android devices with linux boxes over USB without doing all the low level USB and MTP stuff by hand.
(Any hardware vendor is OK, Samsung is only an example)
You don't need any special software. On recent Linux distributions such as Ubuntu 13.04, all the right drivers for MTP are installed by default. When you plug your phone in, you get a file manager window that shows the contents of your phone. The phone appears as a normal directory, so you can drag-n-drop files, use rsync to sync files, or anything else you normally do to move or manage files.
Some apps, such as Shotwell (for photos) and Clementine (for music) also detect that your phone acts as a media player, and offer specific functionality for syncing a music collection, transferring and processing photos, in a high-level interface that works on playlists and albums instead of just files. You don't need to use this kind of software, but it's there if you prefer not to worry about exactly where each file is stored.
On older Ubuntu versions and some other distributions, you might need to install one or more MTP-related packages through the package manager to make this work. You still don't need any hardware-specific software, and the forum or manual for your distribution will explain exactly what setup is needed.
libmtpormtpfs.libmtphas a cli interface for accessing devices using the MTP protocol, if you want to do more than just mount.