I think you should go with Skylights as it creates an environment that is comfortable to be in -- both physically and emotionally. Additionally you can enjoy of natural lighting and improved ventilation from an opening skylight that makes any room simply feel better to be in.

roof without leaks is number 1 priority and although we loved our old Velux roof windows they leaked over time and were too hot on hot days and the blinds are very expensive so they were replaced with Solar Skylights and, although not as pretty as the roof windows and having no ventilation they can't leak because there's no hole in the roof and operate as a solar powered "light" connected to a small roof mounted solar panel with fibre optic cable (our two 25cm Solar Skylights do a great job brightening our 5 x 7 m kitchen dining area and cost about $500 with DIY installation..

We installed a skylight over shower (velux fixed) in a tiny ensuite and I would highly recommend. It looked absolutely amazing and was heavenly to shower under the sky. We only had the house for a year and sold it (about to install another skylight over shower in our new house), so I can't comment on the long term, but no mould problems or condensation drips. I think if anything the sunlight was actually helpful to dry up moisture. We live in Tasmania so I'd doubt condensation dripping would be a problem elsewhere. We had a fan installed not in the cavity with the skylight but just on the ceiling next to it. In the second bathroom we put in a skylight over bath and put an extractor in the skylight cavity as the ceiling was higher. Could not feel a draught- so I think the question of where to put fan really depends on ceiling height. Do the skylight over shower!! You will not regret it. It really takes your bathroom to another level and there are really no maintenance problems if installed properly with custom flashings. I found velux quite repellent of dirt etc, we did not need to clean after a year (one flat roof skylight, one very large sloped) and I have seen velux skylights looking great with no cleaning for 7 years plus.

I like the middle pic -- the lounge at the front feels right , while the dining and kitchen gets a good view and light , moreso from the rear sliding doors . Having said all of that , have you considered demolishing that ( presumably added on later ) laundry and rear toilet -- it looks like you have 'walled' in the doors so you don't see the 'mechanics' when sitting in the alfresco -- that would give you more options ? In fact , depending on why you want an alfresco , you could possibly almost have 1 dining area , with large opening doors and lots of light , maybe even part of it with a clear and/or skillion roof , giving most of the advantages of airiness but also protection , way easier access to a new 'indoors' toilet , maybe a direct-to-outside door on the new laundry ( depending on where you put it and how big a rear deck you have etc ) . It would give you a lot more options , feel roomier , possibly for a similar budget as your present plans . Just a thought .