First, energy bombs have gone. You can't now lure a couple of dozen pirates into attacking you, blow them away, and steal all their stuff for 900 credits. You can still get cascade mines, but they are MUCH more expensive and can be outrun by a cunning pilot.
Which takes me to point 2. The AI is considerably improved. That may partly be the effect of the faster computer, but I think that pirates are coming in a bit more cleverly and taking better evasive action. They can also equip their ships with side weapons etc. and do anything a human player can do.
Third, the cloaking device stops working within a second or two of being switched off - in the previous version you could flick it on for a second and everyone would forget you existed. Now they just go "OK, he's back" when you switch off and start firing again, which is a lot more plausible.
According to the web site there are other changes - better shields for the Thargoids, for example.
The reason I say that these changes make sense is that (a) they are mostly going to affect the most experienced players who can afford toys like energy bombs and have been around long enough to snaffle a cloaking device and (b) they would be essential if there is ever a multi-player version, which I suspect is one of the goals of Oolite development. There isn't an add-on for it yet, but I'm sure it's coming.
If you don't like the changes you can switch back to strict Elite compatibility, but I'm going to stick with things as they are. And once I make Elite, which won't be long, I'll start playing with some of the add-on packs and see what the game can REALLY do.