I'd definitely recommend grabbing the Transformer if your primary purpose is reading pdf's. I can't really comment on anything else because that's what I use it for and I'm very happy with it. I still need to pick up the dock/keyboard for mine and once I have it maybe I'll use it for chatting, email etc. but I don't really like typing on a touchscreen so I generally avoid anything that involves a lot of typing.
Well it sounds like the only multi-touch gesture you can come up with is zooming and I'm pretty sure that's already been answered by myself and a few other people.
To take this back to the original point again, there's still no reason why you can't dock a touch screen device, in the end if you chose not to use the external inputs that's up to you and by allowing external inputs you can use a regular mouse and keyboard or maybe you want to get a big touchpad that supports multi-touch. I know personally I'd love the option of having a dock and being able to use external input devices with a tablet if I had one, it makes it more than just an e-reader which is the only thing I'd use a tablet for right now.
I'm pretty sure that's again easily handled with the directional input being handled by the mouse and the button being a button on your keyboard. So far I haven't seen any example that can't be handled with a keyboard and mouse. The OS of a touchscreen device does a very good job of making the input method transparent to the application in order to avoid these problems.
In the end there's no good argument for not having the ability to dock a tablet, there's no problem that can't be solved and if you have a couple apps that don't work well with your external input devices you still have the option of using them with the original touch screen or adding on another input device that emulates the touch screen input like a track pad on a laptop, mine supports multi-touich and is exactly like putting your dirty fingers on the screen.
Some applications make use of multitouch gestures, for which I see no general analog on a mouse. For example, how do I pinch to zoom with a mouse?
I think you're missing the point, a touch screen is just a way of pointing and clicking and requires no extra work to support clicking on a screen with your finger or with a mouse, all of that is handled by the OS. The very few mutli-touch gestures I've seen are also easily supported with a keyboard and mouse. Any good developer writes their application to work with or without multi-touch, look at Google maps again, you want to zoom in but don't have a scroll wheel or a touch screen then use the zoom slider along the side.
You're right of course with your last point, it's possible for a developer to not support certain input devices on purpose. In general they'd have to go out of their way to make an app that doesn't work with a mouse though since touching a spot on a touch screen is the exact same call as clicking a spot on the screen with your mouse. I do have a touch screen on my laptop and while I don't use it because I don't like smudging my screen I can use the screen or the mouse with many applications and those have never been designed specifically to work with a touch screen either. I won't argue the point that it's possible to develop an app that doesn't play well with classic input devices I've seen lots of horribly designed web pages and applications that don't consider usability at all.
Link to Original Source
Link to Original Source
Microsoft Research Releases Tools to Help Science Progress Toward an AIDS Vaccine