Of course, I prefer separates. But they can be more expensive and require more time to obtain the proper components.
Also, unless the integrated has an inboard volume control (possibly more hum), one loses the advantage of fewer ICs, and may expend more money for a volume control device. Thus cost may not be such an issue.
An "integrated amp", by definition, has a preamp stage combined with the basic amp. (Check articles in Library of Congress, Stereophile magazing etc.)
Thus an integrated amplifier has more stages than a basic amplifier. This causes problems when a common power supply is used for two or more stages (typically the case).
I removed the first stage from my amps (when I get a descent chassis, and time, I will again offer an amp. Right now, my test amp has two stages) and made a separate preamp.
I have found that to manufacturer the best preamp stage, one needs alot of space, which could not be incorporated into any integrated amps I have seen. The same appears to be true when incorporating a tube analog section into a CD/DVD player.
Separating the preamp from the amp has several advantages over integrating.
1) No signal/musical frequency dependent feedback/mixing between the amp stages and the preamp stage(s). On integrateds, this type of feedback can be seen using an oscilliscope. I have an article on the subject at:
http://www.sasaudiolabs.com/theory8a.htm .
(I tried to make the article easy to understand.)
2) A: Let me mention first; normally an integrated amp comes into existence by designing the output and driver stage(s) to match a given speaker. Then the "preamp" stage is designed to compensate for weaknesses in this "basic" amp/speaker combo.
This causes problems in that the speaker and amplifiers are both variables. (I say the amp and speakers are each variables in that there is no way to directly check each for neutrality, VS a straight wire.)
Who knows how good each is? So now we have three variables, the "preamp" stage, the amp stage, and the speaker. None of the three is neutral as they should be, so trying to obtain synergy is very difficult.
The other way for a manufactuer to create is to design the preamplifier to sound like a straightwire (a stage that can actually be compared to a straightwire). Thus the preamplifier stage is Not compensating for any weaknesses of the amp and speakers. So one less stage to deal and worry about when choosing an amp and speaker.
Now the amplifier and speakers are designed to match the preamplifier. As a manufacturer, comes the back and forth routine of continuing to "tweek" the source, amp, and speakers until optimum sound of the audio system is achieved. I believe this results in a preamp, amp, and speaker combo that has better synergy, with less and fewer weaknesses and more strengths, thus more involving sound.
One thing I have noticed is that feeding a signal from a separate excellent preamp into an integrated amp "input" (usually tube) almost never sounds great. This is because neither the "basic" amp nor the preamp section of the integrated are designed to sound like a straightwire. The internal preamp is off, compensating for a flawed "basic" amp.
Of course a customer will probably not be able do the above procedure as a manufacturer does. But the crucial point is to start with a separate, excellent preamplifier. This gives the customer a head start in achieving a better system by demoing his preamp with different combos at the audio store. IMO, starting with the opposite, the amp/speaker combo and then the preamp will lead to dissatisfaction.