I started with requirement of reading and writing files in from/in a directory on a remote Ubuntu machine.
First, I wrote a Java program that could read,write files
If you want to access a filesystem on a remote computer, then this computer has to make his filesystem available with a service. Such a service is typically a background job, which handles incoming requests and returns a response, e.g. for authentication, authorization, reading and writing. The specification of the request/response pattern is called a protocol. Well known protocols are SMB (or SAMBA) on Windows or NFS on UNIX/LINUX. To access such a remote service you mount the remote filesystem on the level of the operating system and make it available locally as a drive on Windows or as mount point on UNIX.
Then you can access the remote file system from your Java program like any local file system.
Of course it is also possible to write your own file service provider (with your own protocol layer) and run it on the remote machine. As transport layer for such an endeavor sockets (TCP/IP) can be used. Another good transport layer would be the http protocol, e.g. with a restful service or something based on WebDav.
We used sshfs. You can add to /etc/fstab the line:
sshfs#user@remoteAddress:remoteDir /mnt/ssh fuse defaults 0 0
and then mount /mnt/ssh
I think RMI might be the solution, you could set up a server an RMI server on the machine you want to connect to, and use your machine a the client.
I would give the client a path to the file this will be sent to the server, the server could then read in the file as bytes and sent the file back to the client.
To answer your question - No, your expectation isn't valid.
Retrieving files from a remote server is inherently reliant on the services running on that server. To retrieve a file from a remote server, the remote server needs to be expecting your request for a file.
The cases you listed in your question (using jsch and sftp, using a sender and receiver Java sockets) that you have achieved already, are essentially the same as this:
File inputFile = new File(
"\\172.17.89.76\EBook PDF");
The only difference is that Java is using the native os's built in support for reading from a windows style share. The remote windows machine has a sharing service running on it (just like Samba on linux, or a java socket program) waiting for your request.
From the Java API docs on File
(http://docs.oracle.com/javase/6/docs/api/java/io/File.html)
The canonical pathname of a file that resides on some other machine and is accessed via a remote-filesystem protocol such as SMB or NFS ...
So essentially "Good old Java I/O" is more or less just a wrapper over some common protocols.
To answer the second part of your question (what is the best I can do to read/write remote files using Java?), that depends on what remote system you are accessing and, more importantly, what services are running on it.
In the case of your target remote machine being an Ubuntu machine, I would say the best alternative would be to use Jsch. If your target machine can be either a windows machine or a linux machine, I would probably go for running Java sockets on the two machines (obviously dependant on whether you have access to installing your app on the remote machine).
Generally speaking, go with the common lowest denominator between your target systems (in terms of file sharing protocols).