I've had both types of sailplan and have to say that the ketch rig offers more flexibility than the cutter rig, especially in heavy weather. Basically, there are more combination available to balance the sailplan with a ketch. It's also been my experience that the mizzen on the ketch is a very valuable sail at anchor (to stabilize rolling and orient the bow to the wind), and also to get out of tight squeezes under sail (you can back it easy, etc...). If you are motoring or motorsailing, you can also use the mizzen as a windvane to reduce the need for autopilot.
Of course, the downside is that you get an extra mast, extra hardware, etc... However, the sails are smaller and easier to handle - hence hardware size goes down (and cost) - but it probably still is more expensive to have a ketch rig versus a cutter rig. It would be interesting to make a detail cost study.
On our ketch, we do have an inner forestay, hence it's a cutter-ketch rig. We find that when going upwind in heavy weather +30knots, a small yankee + staysail + mizzen (1 reef) is a great combination that will allow one to lie close to the wind for hours (days) and not even needing to use the autopilot or the windvane. Of course, it all depends on the boat's bottom geometry as well.
Downwind, we can set 2 spinnakers (main +mizzen) with small staysails and really get going.
I think the most important aspect when designing the ketch rig is to make sure that there will be enough room between the mainsail and the mizzen to maximize the efficiency of the mizzen. Otherwise, you'll get too much turbulence from the main and the mizzen will not be very effective. Furthermore, a lot of time should be spent on the deck layout to optimally place hardware since there will be a lot of possible combination of sail configurations with the need for a flexible arrangement that will not clutter the deck. I think that will be your hardest task if you do decide to go with a ketch rig.
Good luck,
Manon
SV Zubenubi, 44' Roberts steel ketch