It depends on what you need.

The Mac Mini is a decent system, and makes a great HTPC being small, quiet and power efficient... But it's not a great desktop system. It has most of the drawbacks of laptops without the benefits.

If all you need is something to browse the web, write an occasional paper, that sort of thing, the Mini can be a good choice. Anything beyond that, and forget it. Of course the same could be said of the 13" MBP. But there at least you have the portability option.

I will say that replacing a HDD in a Mac Mini is a royal PITA compared to a MBP. It's very very easy on a MBP, and all you really need is a Philips #00 screwdriver. On a Mac Mini, especially the new ones, you run the risk of damaging something that is very expensive to fix because there are these vertical insert JST connectors which will just fall apart at the slightest provocation. And the new Mini's have a thermal sensor literally soldered directly to the drive. So, unless you did a permanent bridge of the thermal sensor, which would void your warranty, you'd have the fan running at full speed all the time. You also need a special tool to slide the logic board tray out a bit to get the HDD out and in again. It's just a real recipe for disaster if you don't know what you're doing.

The only thing that's really user upgradeable on the new Mini is the RAM, which is a step up from nothing on the old Minis. On the MacBook and MBP, RAM and HDD are considered user upgradeable parts.

Only you can decide which is best for you, but hopefully some of this info has made it easier to choose which one.