I think they are (or can be) fine, but they are a "warm weather" option. By that I mean that if you live somewhere that experiences below freezing winter weather, you might have problems with leaks.
I know of a few people who have had problems with them (Volkswagen Golf, some other North American vehicles).
Another factor to consider is indoor storage, that will probably make it OK for northern climates, but if you park outdoors and live with winter, I'd avoid them whenever possible. It's not just the drains ... you can burn out motors or mechanisms if you try to open them when there is frozen water in there somewhere, and even in cold weather the top of the vehicle tends to melt, then freeze when you shut down. Replacement and repair is expensive.
The other thing is, do you actually want a sunroof? Some people don't use them or see the value, and it's not an inexpensive option (even if it's included). The issue will come up if you are buying new with premium trims, where it's a default that you can't avoid. You might be able to option the car out as you like by choosing a lower tier model, and that might mean higher cost since packages tend to offer at least some savings, but automakers tend to reserve certain interior trims, leather upholstery, etc for only higher tiers. I guess you will have to decide which way to go there.
Unrelated, somewhat, but the same issue arises if you don't want nanny options like automatic braking, although that is / will change shortly where you won't have a choice due to regulatory requirements.