Prices are actually lower because of the financial crisis, especially at more expensive hotels. You can find some amazing bargains if that is what you want. Smaller places can't discount as much as they are struggling - many of them are small, family owned businesses coping with higher energy costs and higher taxes. I actually expect 2013 to be "the" year for great prices and then I think we will see them start to rise back to more normal levels in 2014. So if you want a deluxe experience at a bargain price, this may be your moment.
The islands you are choosing are very pleasant, stable places. Occasionally, they might be affected by a ferry strike or other transportation strike, but they are otherwise nearly immune from protests and other problems.
Santorini and Mykonos are also usually two of the more expensive islands, so the drop in prices may really help make your trip more affordable. You will already be traveling relatively early in the season, when rates are low, but you may find that you can afford a better room or go up a class in hotel. Go for a caldera-view room on Santorini - unless you have a bad head for heights, you won't regret it. The view is stunning.
Athens is the only potentially tricky part of your itinerary. There can be transit strikes and protests in the downtown area, but I expect there to be fewer of them in 2013 than they were in 2012. You may want to plan your trip so you have a day in Athens at each end of your itinerary so you have two chances for sightseeing, in case the first opportunity happens to coincide with a strike or protest - unlikely but still possible. It's a good idea to have your last night in Athens anyway, rather than trying to make a connection from an island back to Athens the day of your flight home.
May is my favorite month in Greece and I think you will find it very beautiful and pleasant. The waters can still be a bit chilly depending on the weather, and on what you are used to, so if swimming is important to you, try to choose dates toward the end of May rather than the beginning. May 1st is a traditional worker's holiday and so it can promote protests. This year, 2013, Greek Orthodox Easter is May 5th and that does disrupt travel schedules, site schedules etc for a couple of days before and after. It can be a beautiful time to visit Greece and see the traditional celebrations, but traveling over Easter Weekend (essentially Friday-Tuesday) can be a bit more challenging than usual as many Greeks try to go home for the holiday, ferry and other schedules shift to accommodate them, and taxi drivers get to charge a surcharge for holiday service. So if you are in Greece at that time, it's best to schedule things so that you are staying in just one place for the Easter period.
You may also want to check out my article The Greece Financial Crisis - How Will It Affect Your Travel? for some additional information.
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