[Caveat: The comments below may sound more informed than
they actually are. Although a moderate amount of knowledge
and some reasoning can derive somewhat accurate conclusions,
the complexities of technology and economics may sometimes
trip up even professionals, so consider the source--a
"hobbyist", not a professional or trained academic.]
In some cases integration can increase reliability (partially
from co-design and more unified responsibility, but more
finely controlled and automated manufacturing and reduced
transportation of sensitive components *might* also be
factors). (Also, on the one hand, thermal expansion and
contraction might be less problematic with shorter distances;
but, on the other hand, the tolerances might be even smaller
and cooling more problematic.)
One factor that discourages integration onto a single IC is
that different components would be optimally manufactured
with different manufacturing technologies.
E.g., current DRAMs use different process technology and
fewer metal layers than microprocessors. It would be
possible to manufacture DRAM in a logic-oriented process
(such is called embedded DRAM [eDRAM] and is used by IBM
in its POWER7), but such tends to be less dense and the
extra metal layers (that are not necessary for the memory
portion) add some cost to the memory and the different
process steps needed for DRAM increase the cost of the
processor (though IBM exploited its trench capacitors to
help in balancing power distribution). In the opposite
direction, implementing a processor in a DRAM-oriented
process has recently been announced for a specialized
product (I do not remember the company or product name off
hand), but such limits the number of metal layers for the
processor and the quality of the logic circuits. (For the
intended use, system performance is limited by memory
bandwidth and parallelism is abundant, so reasonably
numerous wimpy cores are not a problem.)
Some of the memory technologies that are under development
are more friendly to logic processes (and in some cases
less influenced by higher temperatures--DRAM generally
needs to be refreshed more frequently at higher
temperatures), so integration onto a single chip might be
more practical in the not-too-distant future.
Aside from different components potentially being more
optimally manufactured with different process types, it
can also be more economical to manufacture some components
in less advanced technology. In some cases, improving
energy efficiency and performance is less critical than
reducing cost or aspects of the chip require a fixed
minimum area (e.g., the size of solder balls has not been
decreasing as rapidly as the size of transistors and some
analog components have more-or-less fixed sizes), so
there can be a cost advantage to not integrating components.
It may also be desirable to separate some components which
communicate with the outside world to reduce interference.
Improvements in integration technology (and increased use)
will likely make tighter integration more common. The
increased fixed costs associated with advanced manufacturing
are also likely to increase the emphasis on mass production
and power density constraints may encourage dark silicon;
both of these factors may encourage integration of components
that are not highly utilized (whether by product [very coarse
grained time scale] or by finer-grained time scales
[assigned purpose--perhaps on the order of a year--to
current task--potentially on the order of microseconds and
smaller]).