There is no avoiding this other than increasing the speed of the device. It's not the OS' fault. It's a hardware problem. The OS can't magically prioritize access to a bottlenecked resource. Breaking up IO to a slow interface is only going to make things worse. You need to move large blocks to be efficient and that takes time on a slow device. Moving smaller blocks of data to allow for "proper disk scheduling" will only make things worse.
No, there is plenty of avoiding it, it is called writing a bleeding smart as a fox disk scheduler. A clever disk scheduler should at the very least under no circumstances allow any process to spam the disk I/O queue. It should be written in a way where it detects that a process is in the process of doing a crap load of reading/writing to the disk and then allow the read/write requests of other processes to jump ahead of the queue, specially, if they are related to system processes, ESPECIALLY!!!!
Combine that with whole hell of a lot more clever rules for how to priorities simultaneous read/write request from different processes and it should be very possible to create an OS where programs that rape the disk I/O can still slow the system down, but not stall it so it becomes so useless that you have no choice to walk away and do something else in the meantime. It is 2008, the concept of multitasking was invented decades ago and yet I have to often suffer through a program giving OS X a joyride in ye old timemachine, back to the time of a single task operating systems.
This is one of the reasons I consistently rail against higher and higher cpu rates while bus, memory and disk speeds remain fairly constant.
Yes, exactly, for the life of me I cannot understand how incredibly little development or focus there has been dedicated to this mother of all bottlenecks in computers. I swear to ye old gods, whenever I hear my hdd having a seizure as the beachball does its hypnotic dance across my screen trying to add a little cheer to the insufferable business of my Mac being rendered useless I am overcome with a strong urge of hammering a screwdriver through my Mac exactly where the HDD is while laughing manically. One of these days I am going to act on it, blast be that it wont solve anything, it will make me feel better dammit.
What the heck do you do with your computer on a daily basis? Sounds like you're hard on your system in many ways. You're right about the system slowing down on certain programs and that's typical of any computer. I have major doubt that you've tried the many thousands of 3rd party software for Mac OS X so think twice before you say "most 3rd party programs for OS X suck". I actually prefer to use 3rd party programs rather than Apple's, they have less bloat than Apple's and updates are generally more satisfying.
I do only 3 things on my and mostly only these 3 things. I download videos from the net, mostly from News servers which then need to be Par checked and unrar/unzipped. I watch same said videos, and lastly I surf the web. I am neither happy with how OS X performs during any one of these 3 tasks nor am I happy about the programs available to do them.
I have tried all available programs that can do unrar, and none of them can even being to hold a candle to winrar. Extremely few of the unrar programs can handle all types of rar file formats and the select few that can are very amateurish in execution. All of them are glitchy and often during unrar land on their asses so hard that I have to use Force Quit to get them off of it.
The only semi descent par check program for OS X is MacPar Deluxe and lets face it, it sucks, very much. Surprisingly it does not have a problem with crashing, but what it tries to make up for in stability it more than fails in performance. If bad performance was a sin then Mac Par Deluxe would be Judas, or an equivalent backstabbing bastard of you favorite religion.
More than any other program MPD renders my Mac completely useless, it makes spamming the I/O queue into an artform and does with a skill unseen by my eyes, on either sides of the fence, and still somehow finds energy to punch both of the proud Intel Core 2 Duo cores of my 2.2 ghz MacBook in the balls. I am windows refugee, so all the programs I use on my Mac I used some other version of on Windows. MPD's windows alter ego is called QuickPar and at least in comparison it is friggin awesome.
When I start the parity check on OS X with MPD all programs become useless, specially Safari which just beachballs for the upto 10-20 min it takes for the parity check to finish. If, god forbid, an invalid checksum is detected and MPD attempts to fix it then go for a walk and leave the windows open. My already overheating MBP becomes so hot that it might as well be a frying pan and forget about using the Mac unless you want to use it as one of them fancy beachball renderers.
The video watching part? Well forget all about Quicktime, because if by some miracle it can actually open the video then it is surely to either stutter or crash. I only watch HD movies, if you are curious, mostly x264 or mpeg2 TS encoded with AC3/DTS sound and often in a MKV container. Quicktime is designed to playback at the very most SD resolution mpeg4 or simple profile H264 with 2 channel AAC audio, and pretty much nothing else. That is all good and well from Apple's point for view, it can play back anything from iTunes reasonably but it is useless for anything else.
I use either VLC or OSXMBC for video playback and the biggest problem of both is stability, specially VLC. Even a gentle gust of wind can sometimes bring down VLC, but at least it has Quicktime beat by lightyears in terms of performance and video codec/container support. OSXMBC has them both beat but it too is plagued by horrible stability and has managed to kill OS X a few times too, something Quicktime is also an expert in.
Other than that I have to say unlike most Apple written programs Safari is pretty terrible what performance and stability is concerned. I have a tendency to have a lot of windows and tabs open at the same time and Safari does not like that, no sir, not the least bit. As soon as the system becomes heavily loaded Safari throws in the towel. It crashes often and it does not seem like it is very good with threading, where I can work in one Safari window or tab as another is doing some heavy loading. If one is overburdened then they all become completely unresponsive and the beachball does its dance.
And aye, all them HD movies are bootleg, just ye try and stop me, I'll run ye though with me pirate saber.
button then deleting.. 
