My number one priority would be transportation. The reason for that is three-fold:
1. People don't like to go on vacation to "wait" for their fun.
2. By decreasing the amount of "wait time" for the guest, you increase the amount of "spending time" they have.
3. Over the long run it would be a money saver.
The transportation solutions would be relatively simple, with the goal being to move resort guests around the property in a more efficient manner. This system would greatly reduce the number of busses in use while increasing the use of more "eco-friendly" and cost effective fuel sources.
As other posters have mentioned the expansion of the Monorail would be a common goal for most of us, but I would only expand it as far as the BWI/BC area. To do this with the least amount of cost I would have the current EPCOT station become just a stop along the way, but it would stop there twice. Once as it travels from the current TTC on the way to the "to be built" station (TBB). It would stop at EPCOT again when it leaves the TBB on it's return trip to the TTC.
There would still only be two monorail loops, but the current EPCOT loop would just be extended to the TBB. To do that in the most inexpensive (and timely) manner I would have the monorail take a gradual descent to ground level for the short trip to the TBB, thus requiring fewer posts for an elevated rail.
From this TBB station I would create two loops of "light rail" that would have the following destinations:
Loop 1 would stop at AK, Blizzard Beach, AKL, CS and the AS resorts (not in that particular order).
Loop 2 would stop at DHS, POP, CBR, Typhoon Lagoon, and the DTD resorts.
There wouldn't be a stop at DTD itself because that would create a problem with "day guests" wanting to park there and use the night rail as their main point of access. There COULD be a stop there if a station could be built that would require a resort key for access to it. I'll work that out as we go along.
Additionally, I would create one other light rail loop from FW and WL to the TTC (or maybe MK...depending on the budget that the Board approves...lol).
The light rail stops at the Parks would be at new points of entry, not the current entry gates. This further reinforces that this is a system geared toward guests staying on property and making their commutes as easy as possible.
The current bus system would still exist, but in a scaled down version.