MIL PLT COMPLAINT ON ATC JURISDICTION IN THE AREA SURROUNDING SJU; PR. POTENTIAL CONFLICTS BTWN MIL AND COMMERCIAL ACFT.

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I WAS TRANSITING FROM TJNR TO W-369 AT 5500 FT (VFR CRUISING ALT) HDG 070 DEGS. I SAW A TWIN-PROP COMMERCIAL ACFT AT MY 9:30 POS. IT APPEARED TO BE A SHORTS 360 AT 5000 FT ON AN IFR CLRNC TO TIST. HE WAS ON A COURSE TO PASS BEHIND ME. I CLBED TO INCREASE SEPARATION AND GAVE HIM A WING DIP TO LET HIM KNOW I SAW HIM. HE PASSED BELOW AND BEHIND ME WITH 1000 FT AND 1/4 NM HORIZ SEPARATION. HE DID NOT DEVIATE IN COURSE OR ALT. IN MY OPINION; THIS DOES NOT MEET THE CRITERIA FOR NMAC; BUT THE SHORTS PLT MAY HAVE BEEN STARTLED. I BELIEVE THAT THE PRIMARY REASON FOR ONGOING CONFLICTS BTWN NAVY TFC DEPARTING TJNR AND CIVIL TFC IS THE WAY THAT ATC RESPONSIBILITIES ARE DIVIDED BTWN SAN JUAN AND NAVY. THE NAVY HAS ONLY LOW ALT APCH AIRSPACE TO S/SE OF TJNR. DEPARTING NAVY TFC -- ESPECIALLY TO N/E -- GET TANGLED UP WITH CIVIL TFC BTWN SAN JUAN AND VIRGIN ISLANDS. WE CAN ASK ZSU FOR VFR ADVISORIES; BUT BY THE TIME WE GET THEM ON THE RADIO; WE'VE ALREADY PASSED THE DANGER ZONE. WHEN WE DO CALL THEM; THEY'RE SO BUSY WITH THE COMMERCIAL TFC; THEY FORGET ABOUT US ANYWAY. RECOMMENDATIONS: 1) UNIFIED CTL FOR TFC E OF 45 DEG 10 MINS W VICE THE CURRENT N/S DIVISION. THIS MEANS FAA CTL FOR APCH/DEP AT TJNR EXCEPT RAPCON. 2) APCH AND DEP CTL AT ST. THOMAS AND ST. CROIX. THIS WOULD CREATE BETTER TERMINAL SVC AND FREE UP CTR TO MONITOR CTR TFC (VICE TERMINAL). 3) STEREO RTES FROM TJNR WHICH SERVE THE MIL'S NEEDS (CURRENT LCL DEPS DO NOT BECAUSE OF AIRSPACE CTL DIVISIONS) AND DECONFLICT WITH CIVIL TFC. ALTHOUGH NOT DIRECTLY RELATED TO THIS INCIDENT; WE ALSO HAVE FREQUENT CONFLICTS WITH LIGHT CIVIL TFC TO/FROM D.J. TORRES AIRFIELD WHICH LIES WITHIN TJNR'S CLASS D. THIS TFC OFTEN DOES NOT APPRECIATE THAT MIL VFR TFC PATTERNS CAN EXTEND MORE THAN A MI BEYOND THE DEP END OF THE RWY. AGAIN; A BETTER DIVISION OF ATC RESPONSIBILITIES AND STEREO RTES (FOR THE BUG SMASHERS TOO) WOULD HELP.