Fractional Jet departure described confused routing clearance to RSW; later to discover ATC was considering a pilot deviation; reporter claiming ATC erred in the routing and that the subject routing was problematic.

Narrative

Our original flight plan was filed as KZZZ..ORL..LBV..KRSW. Our clearance was Radar Vectors LAMMA Direct BITHO direct. As we taxied out ATC wanted to clarify our route; LAMMA BITHO direct; which we confirmed. As we approached the end and called ready we received a new clearance; runway heading expect Radar Vectors RSW. In the air and switched to ZMA we were given a 140 heading. After flying the wrong direction I queried ATC on how long on this heading; he responded; 'I don't know why they sent you this way?' after that we received a 180 heading; then the Controller cleared us direct MOMMO. We were switched to Ft. Myers and as we were crossing MOMMO the aircraft had just started to turn towards RSW VOR; when the Controller asked if we were on the SHIFTY Arrival. We answered that we were not cleared an arrival. The Controller responded OK; turn to a 240 heading. A few moments later the Controller came on and said no fault of yours we are just trying to get this straight; what was your clearance; which we explained as direct MOMMO. He said contact Fort Myers; the flight continued to the airport with no more comments. After being on the ground; Ft Myers called me and asked me to contact Miami Center. I called and he asked me about the flight and clearance. I explained as above the numerous changes. He stated that he listened to the tapes and said everything you said is correct; you were not cleared via the arrival even thought the Controller had put it on the strip. His only concern for me was why I did not query the point after MOMMO. He then went on to say; 'let me think about this and whether or not to file a pilot deviation.' I explained that I would need to file a report and would like to know. I told him that I thought it was unfair considering that his Controller put the arrival on the strip and never cleared this way. Suggestions; I have encountered numerous complaints to the SHIFTY1 and think that is needing a overhaul.