I can remember two occasions when, having been planned over Afghanistan, I finished up coming via the Gulf; situation one, advised by Pakistan ATC that my current level, FL310, was unavailable and I was to expect FL240 at the IFR boundary with all higher levels blocked, re-planned in the air via Bahrain, maintained FL310 and got climb to FL350 from Bahrain, arrived LHR with a bit more than normal reserves plus LHR 20mins.
Second occasion was routed on a very southerly route over the Bay of Bengal and India, due congestion on the more Northerly routes, also a screaming head wind, heading for Muscat and Iran, advised by Muscat that Iran had closed their airspace, just made it to FL350 over AUH before the re-routed Northerly traffic all came up on the UAE frequency fighting for levels!
Normally the route chosen by Flight Planning will be the one that uses the least fuel, subject to ATC availability, closures etc.