Well, fewer locations is a tradeoff, too: less moving around gives you more time to spend in the places that you choose, but doing day-trips out-and-back involves more driving, and having fewer "bases" tends to limit the places you choose to go. So it's a tough call.
We flew into Bastia (arriving late in the day, just before sunset), picked up our car and immediately drove straight to Saint Florent. We spent 4 nights there and used it as our base. Spent the next few days in Bastia, up and around Cap Corse, in and around Saint Florent itself, and nearby spots to the south/west. After Saint Florent, we headed west along the coast, and followed the coast all the way around to Bonifacio. Here's a rough map showing were we flew in to, out of, and where we spent each night in between. Corsica Map - Flights & Accoms ("moon-and-star" symbol indicates each overnight). As you can see, we spent a good portion of the trip (roughly half our time) along the west coast (which we loved). But we pretty much skipped the entire east coast south of Bastia, and I'm sure there's great stuff there, too.
You could probably do L'Ill Rousse and Calvi as a day trip from Saint Florent (remember, we spent no time in L'Ill Rousse so can't judge how worthwhile it is, it did look intriguing). That would probably be a long day in the car (out-and-back) so be realistic and kind to yourself, after the (presumably) long flights to get to Corsica.
The places that really wowed us most were primarily along the west coast, and Bonifacio (we liked the other places too, but the west coast and Bonifacio were the places that left us slack-jawed in awe). You're not doing the west coast, but maybe there's equally good stuff on the east coast, and the interior looked very attractive too, when we blew through it (it took us most of a day to drive from Bonifacio to Corte, and we could see the mountains looked great).
We had 3 nights and two full days in Bonifacio, and could easily have added another day there - but I wouldn't want to have taken it from anyplace else. The eternal rub of prioritization, trade-offs and hard choices. "We should have given this trip another week" is a phrase I find myself muttering at the end of too many trips.
We flew into Bastia (Bastia by far has the most flight options) and we flew out of Calvi (only because there was a unique flight there that got us straight to Strasbourg, which was part of an elaborate scheme to get home - long story, but it all gave us a few "bonus days" in Alsace, which was very nice, but an unconventional way to get back home to Seattle that many would call crazy). Calvi has relatively few flights, we just found one that worked well for us. Both airports are pretty easy to deal with.
Hope this is useful. have fun.