High on that list by Ceber should be the commute. As a pretty much life long Minnesotan, nothing is worse then the 1 hr plus drive from here to there. Driving from one suburb to the other IS time consuming. I'd also agree you should have a real idea on where you would like to live. Neither area is all that bad, it just depends on how, where, lifestyle type of things you want. They (twin cities) are different, night and day. Answer some of the things Ceber brings up and you could reduce many areas in the "cities."
I'd look into Summit Ave, in St. Paul. Very nice and old school. Kind of a yuppy type atmosphere, but is still tolerable. Pretty much in the thick of things, with Minneapolis about 10 minutes away and the X on your doorstep, not to mention all the schools near. Hard to explain how nice the area is...I'd check there.
I have to agree with Summit Ave in St Paul. Your 10 minutes from downtown Minneapolis (20 during rush hour). The houses are very nice older homes and the Xcel Center is 5 minutes away if you can get tickets. Whenever I'm in the area everybody seems to be either jogging or riding a bike.
As for schools Macalester, St Thomas and Hamline are all nationally respected private colleges or the U of M is about 10 minutes away.
I say thumbs down to Summit Ave. St. Paul if you are working in downtown Mpls. 94 often is a parking lot between the downtowns at rush hour. Moreover, I can assure you that it takes 15-20 minutes just to get on to 94 from downtown Mpls at rush hour. I work in downtown Mpls, and it is a nightmare getting to the X (which is near Summit Ave.) when they do 6:00 starts (and sometimes 7:00 starts, as well). I would suggest Linden Hills in southwest Mpls as one of the nicer leafy urban neighborhoods you will find. South Mpls around just to the west of 35W at Diamond Lake Rd. is one of the best commutes going. SE Mpls near the U of M may be good with a student in the family.