One of the things is that the first few versions were marketed by both SubLogic itself and Microsoft.
Microsoft serviced the IBM PC (including Tandy and NEC) and Apple Macintosh, subLOGIC "did" the rest (Apple II, TRS-80, C64 and Amiga, Atari 400/800 and ST, MSX and a few others).
The chronology in short:
Jan 1980: subL FS1 for the Apple II (with the 4-color images) - in time there were 3 releases with increasing scenery complexity (Flight Simulator 1)
Mar 1980: subL FS1 for the TRS-80 - with the crude b/w images: seems odd, but it is indeed released after the Apple II version, as the manual explicitly states
Oct 1982: MS FS 1.00: the first of the "second generation" with the "complete" cockpit with 6 gauges, engine gauges, comm radios and "real" scenery, The green cover (Don Schaaf) is from that version
??? 1983: subL FS II for the Apple II, in early 1984 also released for the C64 and Atari 400, also belonging to generation 2, similar but improved version of the MS-FS 1 for PC (ADF added, more and better scenery) (Flight Simulator 2)
May 1984: MS FS 2.10: a game of leap-frog between the MS and subLOGIC releases, MS FS 2.1 being an improved version of the above FS II
??? 1986: subLOGIC releases FS II for the Atari ST and Commodore Amiga. Similar to the above, but much improved version, thanks to the much better processor and graphics. First version with multiplayer. Very similar in functionality and graphics to the much later (Jun 1988) MS-FS 3.0 for the PC. Together they form generation 3 of FS. That's why I prefer to call the ST/Amiga version: FS III
May 1986: MS (not sL) releases FS 1.0 for the Apple Macintosh. Similar to the FS II versions for the Atari ST and Amiga, but only in b/w and no multiplayer
You can see some descriptions and screenshots of the different versions at my FS Vault website, see below
Jos Grupping (FS Historian)
Flight Simulator History http://fshistory.simflight.com/
The Old Flight Simulator Vault http://fshistory.simflight.com/fsvault