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I'm happy you liked it, and thanks for your question. It took a while to answer because I had to check the code :)

The Anniversary edition is a port of the Pico8 version, which is, in turn, a port of the "TOS" version, so the improvements made for the TOS version are there: distances and torpedoes are calculated using trigonometric functions, and objects (stars and Klingons) are persistent, which means their positions and energy levels don't reset each time you leave the sector (as they do in the original Super Star Trek).

In the TOS version (and in the original version), Klingons move when the Enterprise moves. Somehow, I forgot to develop this in the Anniversary version, but I added it in version 1.13, so the two games are now aligned. However, this Anniversary version was playtested a lot, and it received some refinements in terms of difficulty level. In both versions, depending on the difficulty level, the number of starbases, the number of Klingons, and the maximum energy level for Klingon ships change. But, the math to calculate these variables is slightly different between the TOS/Pico8 and the Anniversary versions (the Anniversary version algorithm makes much more sense). Also, the algorithm that calculates the chances of damage, how damages are repaired, and how the difficulty level affects damages, is entirely different. The TOS version uses the original algorithm, which is very complex and honestly doesn't make much sense (for example, regardless of how much the system is damaged, it always takes 10 days to repair it). I simplified this in the Anniversary version, but this part should be refined even more.