I totally agree with Undertow and Grannyring. That too has been my experience with passive and straight-into-the-amp sources...something is always missing and that something has ALWAYS translated (for me) into a flat, dry, and smaller sound than going through a good preamp.
Itsalldark, you said:
"When you put a pre amp into your system you are now listening to music that has been changed by the manufacturer of said pre"
That basically says nothing or everything, depending on your view point. The result of any signal passing through ANY component is changed from input to output by some degree.
As we all know there are those audiophiles who desire to re-create the exact (but amplified) copy of the what was captured in the recording studio (unless you were in control of the mixing process you fail this quest at this step) in their homes...and feel that any component that colors the signal is bad (even if that results in a beautiful sound)...of course its not possible to re-create this signal with 100% accuracy and it's also something i happen to not care about. What I care about is good sound, and if, for example, a pre-amplifier's colorations result in my increased listening pleasure then so be it.
After spending thousands on gear...give me "colored", interesting, musical, sound anyday over analytical, dry, mechanical sound, even if that accuracy is objectively a closer correlation with the captured waveform in the studio...bottom line is if it sounds good to my, yours, or his ears that's all that matters.
In keeping with the theme of this post, I have yet to find a truly great/captivating sound with any pre-amp less system. It would be sweet if that were the case (who wouldn't welcome one less box?), but so far in my experience a pre-amp has always improved the perceived sound quality. YMMV :)