Residence Inn is an extended stay hotel, it includes a kitchen with full size appliances. The last time I checked with points, you earn less reward points at RI. The rooms are big and comfortable. Aside from the kitchen, there is also a living room area with a full size sofa, easy chair and most have fireplaces. There is a desk but in most of the ones I've been, the desk is in weird location, sort of makes you feel like you've been relegated to the corner of the room, although you do have a window.

There is a free breakfast daily and manager's reception M-F.
Courtyard is a traditional hotel room. The rooms are average size rooms, no fridge or microwave; although I did find out at the courtyard I'm staying at now, they provide free fridges if you request one. Courtyard does not have the free breakfast, although status may get you breakfast tickets - not sure about that. There's no manager's reception.
If you're going to be there for a short term (as in weekly trips under 3 months), I'd probably go with a Courtyard. Longer than that, you might want to consider the RI and work a deal for staying checked in over the weekends.
The deciding factor though might be if you prefer to have the kitchen should you get tired of eating out and want to keep things in the room.