With regard to Macs, none of the software I use in my day to day work will run on Macs.
** Yes, of course it will. I run lots of Windows software on my Macs. Read the previous posts regarding VERY good virtualisation.
Lets start with the ipad. iOS is buggy, not necessarily to everyone, but my experience with iOS has been like many others, persistent annoying bugs that seem to compound as various versions are released. My iPad at latest release iOS 5.01 is almost to the point of being unuseable.
** Your experience Phil. "Unusable" sounds like a problem with your device, and that's ridiculous. Get it fixed. Restore it and start again. It isn't a painful exercise. Take it in to an Apple shop next time you're in Melbourne or Sydney. I'd be interested to see how you've managed yours, and learn why it's degraded to the point you say it has.
The computer upload/download interface (itunes) and filespace within the ipad can only be described as a dogs breakfast.
Simple acts such as sharing the same file between apps can be difficult or impossible in some cases. Compartmentalised storage is a PITA.
Deletion of images from within the iPad can be easy or difficult depending on how the image arrived in the device, IMHO that's just plain stupid.
** Granted - it's a little messy yet. I think that this will improve over time - it has to! 
I don't mind it on the Mac, but the Windows version is still lacking in some areas.
Flash is not available, no amount of denial by Apple will convince the masses that this is a sensible move.
** Again - Flash is dead on mobile devices. Adobe themselves have realised this and won't be developing the platform for ANY mobile device shortly. The masses are use going to have to adapt.
Batteries are not easily user replaceable, once your battery gets tired be prepared to be gouged by apple for a replacement, or risk dismantling your toy to replace the battery.
** Like any battery, I guess that usage patterns between people are different. I don't use my phone all day every day, so I suppose that someone who does will see shorter battery life. I suspect that ALL phone manufacturers would "gouge" a client who walked into a retail store to have a battery replaced. Admittedly, there is a labour component here as well. As stated, these batteries were never designed to be replaceable - preference going to controlling the bulk of the device and knowing that LiPo batteries are easily going to, on average, last the life of most user's phones.
Now for the iPhone, basically an ipod touch with a sub standard phone and GPS inbuilt, my 3GS had the poorest audio quality I have ever heard from a cellphone. Given it's lineage, the iPhone is well and truly overpriced.
** Interesting. Depending on what network you're on, and where you are, I've found that all phones behave (sometimes radically) differently. I remember Humayun and I tested internet connectivity over 3G when we were at BSG in 2009, and my phone had vastly superior comms to his - and the only difference was our choice of carrier.
Once again subsequent software releases make the iPhone sluggish and buggy.
** Uhmm... you sure about this? Others seem to be OK. I'd dearly love to see your devices. There has to be a reason they're both giving you trouble like this, because it certainly isn't normal. If it were, they wouldn't sell. The 3GS is getting a little long in the tooth though. Software advances unfortunately out-pace hardware design, and it's a fact of modern computing.
As with the iPad, battery replacement is all but impossible for a non tech head and if your usage is high the battery will be tired in a little as 12 months. The plus points are once again the interface, intuitive and easy to use, it just works, that's why I'll be getting another iPhone despite it's flaws.
I love my iDevices, but I'm under no illusions as to the flaws inherent in the devices, nor am I prepared to accept the contempt with which Apple treats it's customers.
** Have they personally treated you badly? Allan here had an almost instantaneous result for his problem. Can't be all that bad... 