There are plenty of Embassy Suites hotels with smaller Polynesian sized fountains, rockwork and plant structures. Some of which not even with very large skylights. The Peabody hotel (the remaining one in Memphis, though Orlando had one until it was recently bought by Hyatt) has a somewhat smaller fountain in their lobby (without skylights), but also regularly allows their live ducks to wander down from their home on the roof to the lobby fountain. Ducks are very messy, but the hotel doesn't mind cleaning up because it's a hotel tradition and the guests love the ducks.
As for the lobby size, properly filtered A/C and dehumidification along with basic cleaning and proper refurbishment (as used to be the standard for Disney) would have prevented most if not all problems that occurred with this. As Disney of late has been trying to pinch pennies with reducing air conditioning for guests along with basic standards of cleanliness and upkeep, these problems escalated very quickly since the mid 90's. If the managers of the Gaylord hotels and Embassy Suites chose to throw their standards of quality to the wayside and instead pursue Disney's current business model, those hotels would rot away in no time as well. They know better though thankfully.
There are also plenty of indoor boat rides at Disney parks with small and very dark rooms, no skylights to speak of, using "swamp water" etc, but I guess we should close those as well because of mold and neglect. Personally though I don't see them closing Small World or Pirates because of the backlash they'll get (they'll either run them to failure until they finally rot away or spend the necessary money to fix them). They also have partially indoor boat rides planned for Avatar and Shanghai Disneyland (at least Shanghai, we'll see if the boat ride makes it into Avatar following potential budget cuts).
