Hey Richard,
yes its a difficult situation but it is all worth it - our favourite experience in South America.
We went in August 2012 (I think this was "dry" season but not necessarily peak for visitors) so not sure how much it has changed, we had been told that the best deals were the last minute deals on the islands so we went expecting to be chased and hounded with deals - this was not the case. Agents there were generally disinterested, they had the deals on their boards for all to see. Chatting with them and others it SEEMED to be that the deals were pretty much the same as what could be found in Quito or Guayauquil. I think they may have been slightly cheaper.
That said we did end up snagging a very good deal, this took a few days of patience and haggling with an agent of questionable repute - the notorious "Freddy" who is often found in these moments. After some anxious moments we called the company (Galavan) who ran the boat (the Archipel 2) and they confirmed they had our booking.
Off memory we managed to get it for around $1,250 down from late deals of around $1,500(on the internet) and we found out that fellow passengers who had booked well in advance from their home countries had paid around $2,200 to $2,500. Ours was an 8 day that began in San Cristobal and visited the main islands and then went around the far side of Isabella.
The boat was considered a high class boat and it was very comfortable, our cabin was quite large with private bathroom. There were only about 6 cabins onboard.
Flights - at the time most were paying around $420US return, after a lot of searching we managed to find some for around $360. Please note we had plenty of time both before getting there and on the islands to make our plans, so if you were time pressed it might be better to organise beforehand.
Our friends also did it the same way and said the savings they achieved compared to what they could have found in Quito was negligible.
If you do choose to go to the islands to find a deal there are worse places to be, food is quite cheap as is accommodation. There are nice beaches and plenty of wildlife.
If you are traveling but time is an issue I would just try and organise it in Quito (better than Guayquil as agents are all close to one another).
That deal sounds ok - park fees off memory are $100, flights around $400 so the cruise is $1,300 but it is tourist class (these classes could be a bit mixed at times), most of the "tourist" classes we saw looked ok.
In terms of your statements - I think deals were easier in off peak times; I thought booking in person was cheaper than internet (maybe 10% - could have changed); Galapagos was only marginally cheaper than Quito there was definitely not a lot of people hanging around trying to find last minute deals; airfares - not sure, I think cheaper yourself if you have time and flexibility; not sure about which operators - logic says boat but do they sell direct?
How much time would you have in Quito to wait and decide - the savings might be used up in extra days there.
