Nothing is stopping you

First off: the sentence should be "Why can't I expect to have the freedom, etc".
Second: Why are you not listening? Nor reading?

You have all the freedom you want to change things around, but you will run in to problems if you do not properly take care of the alterations you made to the way things are usually organised in the Linux hierarchy.

Hierarchies usually don't fall out of the blue sky for no reason, and some of these reasons have already been mentioned in this thread. If you want more reasons and ways around this hierarchy, study the links I provided earlier.

If you do not like to investigate people will soon grow really tired of repeated questions. After all, we are no answering-machines.

@TiagoTiago

Try to understand following: As you can see from anthonie´s picture programs are not usually installed to ONE directory. They are scattered across different directories.

Moreover what do you gain from if you were able to install program to ONE directory. You could surf there with explorer or from cli and then what? What do you gain from all that? Now you have filesystem that puts config files to one directory (generally in your home directory) and executables to another. Actually IIRC home directory has been for ages place for different config files so if you backup ONLY your home directory you backup also all program settings. If system crashes just install everything back and pull home directory backup and you have specific programs back to configuration what you had before crash.

And as said you have total freedom because of symlinkin.

Optification is something that is specific to N900. No need to worry. Just use apps from extras. If you choose to install stuff from testing and devel, then as their description says, test and report and fix by yourself. And I bet that if we had option to choose where to install then quite many N900 would be pretty much breaking all over the world because of user errors.

Linux doesn't have anything to do with the way you install software. (In fact, it will not even know about software installed on your system.)

How it works is entirely up to the distribution and its package manager. The fact that distributions do follow the well-established standards here speaks for itself.

Still you're free to do it differently no matter which distribution you choose.... If nothing else helps, you could even re-compile the sources and give a new installation path.

Usually, things that restrict your freedom and could be done in a better way are instantly addressed by the community. The issue you brought up did not, so far, result in alternative package managers which include a "install in..." option. I therefore assume that what you propose was the initial problem and the situation we have now is everybody's solution to it.

Linux gives the user power to make a mess in so many way....why the need for additional steps just to change the install folder name or location?

I much rather how Windows installers work, by default they install where everyone installs, but they give you the option of doing differently at install time, without the need of recompiling things nor doing manual changes after the installation.
edit: oh and there is even a trend now for also offering the option of keeping config files in the install folder instead of in the shared folder for config files

I have to agree somewhat with OP. An install here option would be pretty nice in some situations. Particularly when you run out of disc space and throw in another drive. I'm not saying I have solution or even that i require one, but sometimes it's annoying.

Why people are not reading?

The optification of the programs is a N900 specific issues. For which there are several workarounds. If you wish to change the way linux handles programs please sent an email to kernel.org. I would love to see the reply to that email .

Windows is a mess of programs thrown everywhere, f*cked up registries and fragementet FS. Linux keeps everything "clean" and in order why are you willing to change this?!

I think OP is mainly bothered with n900's partitioning issue (with the 'optify' workaround) and proposed a solution from something that he's familiar with (which unfortunately comes from the windows world).

So... let's not overreact..

Hmmm. Might this has something to do with that in windows users generally like to make couple of different drives C/D/E and in linux environment people usually use whole hard disk without partitioning it (only perhaps home dir and swap of course).

.edit
And in the end we are fundamentally talking here about core of linux and how it´s File system is made and how different modules of apps are laid across file-system.
http://linux.oneandoneis2.org/LNW.htm

Why a centralized registry is worse than a bunch of files in a bunch of folders?