Flash is definitely a big problem, but it's probably about #3 on my list of gripes.
#1 - Why did apple forsake the concept of a filesystem? Sharing files between apps is a serious pain due to this. You can use stuff like drop box if the app(s) actually support that, but if not you're kind of SOL. Saving things and then putting them back to a windows file share is problematic due to this as well. I can get them off with File Browser. But getting them back after you edited with Quick Office or something means I have to save to my drop box, go into the drop box app, and tell it to copy it back to File Browser. It's really pretty horrible.
#2 - The apps on this thing kind of blow. For all the talk of flash being some gigantic security hole, Apple doesn't seem to have a problem with apps like Quick Office which shared out my files for the world on the default installation. With no security whatsoever. Just use your browser to hit port 4242, you can download any file you please and even modify and upload back if you like. Just the ones in the app itself mind you, because of problem #1. There's an option for authentication, but it's disabled by default. I got a sling DVR from Dish Network, and the ipad/iphone/ipod app for this completely suck. On my PC or the Droid I can actually do things like skip forward. I do this on the ipad app and it freezes the thing and then confuses my box. Just exiting a video can do that at times. It's not perfect on these other platforms, but it's not virtually worthless like the Apple versions. You can blame app developers for this if you like, but the fact that it works on other things makes it seem like Apple really limits what a developer can actually do.
#3 - No flash - that sucks.
I'm sure I can come up with more, like the Wifi settings completely sucking if you are using a network without a broadcast SSID. They're the only ones on the planet that seem to think it's a good idea not to cache this information in case you connect to another network and want to come back. But overall this is my list of biggest gripes after playing with it for a few weeks.