BB email gives you the option to delete mail on the device and server, or on the device only. This is something that can be very handy, but can't be done in WP. Ironically, it's the "full sync" feature that gets in the way. I get plenty of emails that I know I won't deal with on my BB, so I leave them on the server to be dealt with later.
As others have already mentioned, WP's notifications are bare bones. No sound/alert profiles. Hopefully this will change, but for now it's not the best.
You can't email an mp3 or upload it from the device.
There's no option to search in an email. This isn't something I use much, but when I need it, I definitely need it, if you know what I mean.
There's no browser option to find something on a web page.
For me, the most annoying thing is that the WP browser doesn't let you set a default font size and then zoom to that size and reflow the text when you tap. The BB does this well, as does the Android browser.
On my BB I don't have to do frequent battery pulls, so I'm not sure what that's all about. But the long reboots are certainly there. They are necessary mainly when installing or uninstalling apps, which isn't something that I do every day, so it's no big deal for me. But I get the impression that some people are constantly installing and uninstalling apps, so it could be a problem for them. WP definitely has a clear advantage there, if it's important to you.
The integration of MS Office and SkyDrive is maybe the strongest point in favor of WP. BB has nothing comparable, and desperately needs it.
In terms of smoothness, my Radar and 9900 are equal: Both are smooth and lag-free. Your 9800 (the OP, that is) is running OS 6. The difference between OS 6 and OS 7 is pretty significant, in terms of performance and overall user experience.
Battery life is better on the 9900 but it's quite good on the Radar anyway. As far as I'm concerned, if there's enough power to get me from when I take the phone off the charger in the morning at about 6:00 am until I go to bed at 10 or 11 pm, it's good enough. Typically, when I go to bed, I have about 40-50% left on my 9900, and maybe half that on my Radar. So both are fine. But I know that battery life depends mainly on hardware, so not all WP phones will be equal.
The BB's native FaceBook app is quite good, and much better than the current WP app, but of course we can expect the WP app to catch up. Growth in WP Marketplace clearly outstrips what's going on in BB App World. Whether that will change with BB10 is anyone's guess.
BB Traffic is an excellent free turn-by-turn Navigator. Nokia Drive is supposed to be even better, but only available for Nokia phones, obviously. I haven't tried any of the paid nav apps yet.