First of all, congratulations!
All sorts of good advice here already. I agree with others that you're doing some very good advance planning regarding this.
A few random thoughts:
1. You seem to have picked your vacation time based on the availability of the Marriott property near Chania, and are accordingly planning on April as part of your beach trip. But are you aware that April is not beach weather in Greece? It might be pleasant, but not warm enough for hanging out on the beach. In planning your trip, whether to Crete or wherever, you might want to take into account monthly climate averages. Here's one of many useful sites for doing such planning:
http://www.weatherbase.com/
2. If you are going to wait several months, then, perhaps you might want to take the honeymoon in May or June, depending on what the likely weather in your destination will be.
3. Good advice from Yoshi that you can skip Athens and fly directly to Crete (and some other Greek islands) from Paris (or other place in Europe).
4. Paris is the most romantic city in the world. Really. I took my wife there for her birthday several years ago, thinking she'd love it and I'd tolerate it. Boy, was I wrong. Just a wonderful city to hand out in, stroll around in, see the sites, sip wine or coffee at cafes, etc., etc. We've been back twice since then. No problem if you don't speak French, though do pick up some basic words such as saying good morning, asking for the menu or the check, etc,. just as a courtesy and because folks will appreciate it. I strongly encourage you to go.
5. If you do go to Paris, or even if you don't, I also strongly encourage you both to get the Chase Hyatt visa cards. After some inital spending ($2,000 each within three months) you each get two free nights at any Hyatt hotel in the world, plus Platinum status (which isn't anything great, but can get you some minor perks). There has to be award availability for those nights, but generally the availability is there if you book far enough in advance. And Chase does have a rule that it won't issue most types of credit cards to folks who've gotten more than five credit cards of any kind in the previous 24 months (or something to that effect), but that might not affect you and might not apply to the Hyatt cards. (You can research this further at the Chase credit card or Hyatt forum here at FT.)
6. And if you do go to Paris and get the card, use those free nights at the Hyatt Park Vendome. Superb hotel in a superb location.
7. Now, if you are in fact spending a few days in Paris (and have I made it clear enough that I highly recommend this?

), do you necessarily want to go on to Crete? Might somewhere closer to Paris, such as the south of France, fit your bill in terms of having a beautiful, relaxing place to go where you can use your points well?
8. I guess I'll add that I just wasn't wowed by Crete as a beach destination when we went there a few years ago, though Chania is a nice (albeit busy) town. Very touristy, with generally crowded beaches. Ironically, the places we liked best were the small inland towns and restaurants we explored. But I offer these opinions knowing that this is something opinions can really vary on.
9.Wherever you're thinking about going, you might want to check the reviews for a given hotel at both Tripadvisor.com and here in the relevant hotel chain forums at FT. FT reviewers tend to, very generally, be a bit more sophisticated, but Tripadvisor has a wealth of info, plus photos.
Hope this helps!