Three major differences I have found:
1. True an iOS jailbroken device can do most things (all?) an Android device can do. But once you root an Android device all the fun programs are in the primary Android market while a jailbroken device depends on a third party app market that doesn't have the same internal quality (I have had Cydia fail on updates more than once).
2. My Nook Color can update itself with new ROMs, while any Jailbroken iOS device requires you to hook it to a computer to update it, then use a computer to re-Jailbreak it IF a jailbreak is available for that OS version. If you have something that is not jailbroken (iPad2) you have to do completely without. Which leads to:
3. Many of the things I like to do (such as playing emulators) don't require rooting on Android, but do require jailbreaking on iOS.
Honestly I use both types of devices and I am not a fanboy either way. iOS is more responsive, is easier to type in (IMHO), has more and higher quality apps. I don't think I will consider an Android phone soon after my Nook Color, as when I need something in a pinch (aka looking up something on my phone) I want it as responsive as possible.
With that said, to me Tablets are not huge phones- I see them to be eventual replacements for most things people use a laptop for. For me that means the closer something is to a traditional desktop OS (as far as flexibility) the closer it gets to replacing other machines.
1) There is more than just Cydia is as much as I can say. You haven't looked deep enough.
2) Technically, you don't need to update if you don't really need or want a new feature, right? And it's not like updates come out every month. On Android, you flash one 2.2 (or 2.3) ROM after the next, but what exactly is the major difference if not to fix a silly bug? Nothing. I have an Android phone so I know exactly what it is. I have been flashing 2.2.1 ROM for the past... 6 months. Nothing major has changed. But the fact that you need to flash a new ROM to change the interface in Android is annoying.
3) Indeed, but I don't suppose you can just run emulators on your Nook without rooting? And some prefer older versions of an emulator, like PSX4Droid 1.7 (not v2). That means some have to resort to side-loading since that version is not available on the Market. And that means... rooting for some phones since stock phones sometimes don't allow side-loading.
Honestly, I use both platforms, but just the inverse of what you are doing. Personally, I have used Android far more than iOS, so when it comes to Android cons, I am much more aggressive, but that doesn't mean I draw everything out of thin air.
The way I see it, I don't believe tablets will replace PC any time soon. It will happen, but the main goal for tablets right now shouldn't be trying to replace PC. It's like trying to break a castle with a snowball. It just doesn't work that way. No matter how much you want it to.
I think tablets have a long way to go before they can replace PC, and we most likely won't see it this year. Or the year after. Not until you start seeing serious investments in software. As they are right now, tablets are little less than web browsing and email devices. But in that regards, I feel the iPad is ahead of the competition because it has far more applications that can aid in productivity.
And if I'm gaming, I would like to play newer games more than nostalgic titles in emulators. I still have the original consoles and systems so I can just use them instead. Or I can get on my PC, which offers a far better emulation experience than tablets ever will. I'm just not big on touchscreen controls to play Marvel vs Capcom.