I have been an assistant manager for walgreens for 3 years, and on a slightly biased opinion...I'd go with Walgreens for sure.
I know a CVS store manager, and a CVS pharmacist...both are not very pleased with how CVS operates. That being, on a store level, both in the pharmacy and front of the store(self service). With my little personal exposure to their stores, I don't care much for how they do things either.
I will say that Walgreens has a superior benefits package(profit-sharing, 401k, vacations, health insurance, stock options, etc.), if you are looking to stay with them in the long run(5+ years). Example: I contributed a simple $400 to profit sharing last year, and Walgreens turned around and matched that with giving me $1240. That's a 3.1:1 match on my dollar.
As for CphT's, Walgreens has introduced our new POWER program. Currently, Orlando is the test market and then Miami. From there, it will be company wide in a few years. Pharmacists are now freed up from phone calls, filling, and distractions....and are allowed to consult patients more. Basically, trying to utilize their expertise in drugs and help the patients on a more personal level. Techs have more control now, and are getting more exposure to the drugs and filling process. Their is a lot more behind the scenes that goes on in our POWER program, but I am not really allowed to talk about it in detail.
I currently have the option to continue on the store management track with Walgreens(still very rewarding), but I have decided I want to pursue my career with them as a Pharmacist. I spend a lot of time in the pharmacy as a manager, and I feel very comfortable and satisfied back there. Furthermore, all the Techs I have talked to seem to be happy and satisfied.
Lastly, both are in a retail environment and anyone deciding to work at either chain will have to deal with the headaches that come along with retail pharmacy. As a lesser of two evils issue....Walgreens wins.