Enthusia also has a clutch button, but that is an aside.
If you are talking about the flat-shifts on upchanges, you can get around this by quite simply lifting off the throttle when you up-shift. A number of people have already posted to say they do this anyway, not for any reason but they feel it make the game more 'realistic' for them.
If you are talking about the throttle blip on downshifts, then its the game heel and toeing for you, as you should when racing (or in my opinion driving smoothly on the road). It has a very good reason, to avoid compression/engine braking, which is not your friend on the track.
Have a read of these, the first is just about compression braking (but helps clear up a few myths on the subject) the second covers its implementation in GT4 and the reason for the Heel and Toe downshifts. Its a fair bit to read, but well worth it.
Compression Braking - What exactly is it for?
Compression Braking - How well implemented is it in GT4
If you have any queries regading these two posts it would be useful if you asked them over in the GT4 & Brakes thread (link in my sig) in the Tuning section of the GT4 forum, as the general GT4 section is not realy the right place to discuss it.
Regards
Scaff