When returning from Praslin for our flight back home, we chose to fly to make sure we made it on time and did not have to spend a lot of time on transfer on Mahe.
We feel it was a good choice, especially since the actual trip was an experience in itself.
The plane is small but feels very safe - and I have a fear of flying, I never flew something this small before. The logistics at the Praslin airport are very simple, but still full-featured.
The flight only takes 15 minutes but offers fantastic views of especially Praslin island. It also very handy to switch from the domestic to the international "terminals" at Mahe, so it does work to save time using this option of transport.
Try to have as little hand luggage as possible, you need to keep it in your lap or under the seat in front of you. There is no overhead room or other handluggage space in the cabin.
When arriving at Mahe, the luggage is delivered right inside the terminal door in a very small spot not clearly marked. Can be a bit confusing.
All in all a positive experience, but a bit expensive (about double the mimimum price of the ferry).