hi John,
Thanks for responding. Given your available time of 2 weeks (without Nosy Be), I think the locations you mention are an excellent choice in the sense that they are standard and generally recommended.
Personally, I don't consider Isalo a must-do. Isalo is for landscapes, but if you're more into species (like me), you could consider dropping it.
I'd also recommend Kirindi if you can somehow fit it in. But I'm not sure if it's on your route. Kirindi only requires a 1 day stay but well recommended if you're close.
Don't have the map at hand, but I think Anja NP is also a possible quick stop (only a few hours).
For me, Masoala would be in the top 3 of locations visited across 3 trips total. It's a stunning forest. But I understand it can be costly to fit in. My advise: if this is to be your only trip ever to Madagascar, do try to plan it in, but not at all costs.
The only tip I have for domestic flight unreliability is to try and stay multiple days at what you consider the most valuable locations. This way not all is lost when things go wrong.
I have to say though, this unreliability never seriously messed up our program. Returning from our last trip was a pain but we never had serious issues in the midst of a program, other than perhaps 2 hour delays.
Hope this helps?