As a UX professional who travels a lot, I love this question. It's like playing a video game in God Mode: you are in complete control, for better or worse. Let's try for the better, shall we?
A key principle I would bring to this design is personalization. If you stay at a hotel that's part of a chain, they should know your preferences. Ordered smoked salmon the last two times you stayed in one of the hotels? Then your next stay the hotel should provide a complimentary serving as a courtesy. Requested a high floor near the elevator? Then the hotel chain should ALWAYS put you in a high floor next to an elevator unless you request otherwise. King size bed, feather pillows? Ditto.
The hotel staff should also be smart as well as helpful. Just traveled in on an international trip? They should provide you with a humidifier and fresh fruit and juices to help you acclimate, as well as a hints and tips sheet on recovering from jet-lag. Traveling with young children? Provide complimentary pool toys along with a note giving the hours the pool is open. And guests should always have a NAME of a person to talk to… Look to service on cruise ships for some good examples of how travelers have "personal stewards."
You may be thinking "Well, all these freebies will cut into the hotel's profit margin!" Yes, but let's look at it from the customer's perspective. Every one of these extra touches are "grace notes" that will make the customer's experience better, and will make them far more likely to stay at the hotel (or one of the hotels in the chain) again. And it's a lot cheaper to keep a customer than to get a new one…
Other thoughts:
Those signs that say "we can offer you toiletries if you forgot them" require the hotel guest to up the phone and ask for these things…. Which is stupid. Just keep a set of toiletries in every room all the time.
Take out all the little signs in the room that say "if you steal X we will charge you for it." treat guests like guests, not potential criminals.
Put all power plugs at waist height when appropriate (like near desks).
Don't put catalogs in rooms to try and sell the bedding and furnishings to guests via mail order. Does anyone ever go, "Wow, I love that comforter in our room, let's buy one just like it!" It's tacky and a waste of time.
Have extra toilet paper and towels in the room, based on the number of guests staying there – again, guests shouldn't have to ask for things like that, it should just "be there".
Provide a REAL coffee maker with FRESHLY GROUND coffee, thank you very much.
Provide a universal set of chargers in the room for the most common devices (iPhone, Blackberry, etc.).
Provide suggested workout sheets in the exercise room, with simple instructions organized around goals.
Give Internet access away for free, for everyone. In the 21st Century Internet access should be like plumbing and electricity… It's included in the cost of the room.
If the hotel has a concierge floor, then offer REAL concierge service, not just lip service. Free drinks, free snacks, advice on local attractions, restaurant bookings… The works.
Optimize the checking and checkout process, and staff the front desk with extra staff to handle peak times based on historic analytical data.
In summary, you probably notice that I have described only minimal changes to the actual "structure" of the hotel room proper, but have focused on the experience that the hotel should provide. That's because there's not much you need to change in a hotel room – it's utilitarian and appropriately so. The key to a better hotel experience is exactly that: the experience that is provided to the guest. Experience matters.