Hmm...what are the pros and cons of owning both a iMac and a MBP?
It's more the pros/cons of owning a desktop and a laptop. Quite simply: if you hate to plug and unplug all of your usb, firewire, display, etc. get a desktop and use the laptop when you want to work elsewhere (outside, friends house, school, etc.). For me the constant plugging and unplugging was getting annoying. I could not grab my laptop quickly when I needed it because I first had to unmount the external disks and than unplug everything. Working with a 30" monitor attached to a MBP was not really something I liked. Due to all the plugging/unplugging the Mac sometimes was doing some crazy stuff to the colorprofile.
I decided in March that the early 2009 Mac mini was everything I needed (already got everything and it was powerful enough) so I bought it. It works really nicely with the 30" monitor and the colorprofile problems disappeared (unfortunately due to a bug in Snow Leopard I now have colorprofile problems again which seem te be fixed in 10.6.2 when it'll be released). At first there weren't any cable to hook up DisplayPort monitors to the Macs mini DisplayPort so I used the notorious and buggy dual link dvi adapter for that. I later replaced it with a mDP-DP cable from Circuit Assembly (one word of advice: get a monitor with DisplayPort and the mDP-DP cable from CA, don't try the dual link dvi adapter unless you like a gamble). I use the mini quite often and when I want to work elsewhere or for some other reason need my laptop I'll use that. Added advantage: I can leave stuff I don't particularly need on my laptop at home on the mini, saves me some diskspace.
The 9400m is one hell of a graphics card; it drives the 30" monitor without any problems and I can even play things like C&C RA3 (not in native resolution, my MBP doesn't quite like that game being played on its native resolution either). It's not a card for people who do a lot more gaming or play games that need more graphical power. I wouldn't call the 9400m crappy. It's a great card but it has its limitations but so does every other graphics card

Most people use the Mac mini as a mediacenter and the 9400m can do this job perfectly.
There are 2 simple things to decide between an iMac or a Mac mini: if you hate glossy/glassy screens than the iMac is most definitely a no go (get a Mac mini or, when power is necessary, a Mac Pro instead); if you need a better graphics card for something like gaming and/or more memory/cpu power and don't mind the glossy/glassy screen than go iMac (else go Mac Pro). However, before you even decide on getting a desktop machine first decide if you even want one or if you want just 1 machine you can carry with you.