What differences have you spotted in the Mongoose OTU, that nobody would have imagined in the CT OTU?
I think "nobody could have imagined" is a tall order. I'm willing to bet someone came up with these ideas before in their own games. But I think the wisdom or creativity to add them is worth a shout-out.
With only CT as my reference (no MT/GURPS etc), I can say the following:
-Connections and rewards for it (although I understand this was an MT thing, new for me)
-Ship Shares (also an MT thing I hear, but new to me. This makes the game so much more fun when you can just buy a ship out the gate without handwavery. Gets the players involved from step one.)
-Expanded Mustering (while they can make life hell, I really like the expanded options that have been presented in Mercenary and High Guard. Retainers, cybernetics, funding, free ticket advances etc.)
-Events (not sure if this was ever done before. I'm a sucker for Lifepaths and previous history. I think this was almost a no-brainer after the career expansions in the later CT books that added more detail. But it gives the players some starting points to fleshing things out)
-Small Craft (I know the grogs hate the different rules for building small craft. I love them. The starship rules were designed with 100 tons as the smallest capable model. Small craft needed love.)
Other than that, I'm not seeing a lot of changes from canon really. It feels like I mentioned it before... a little glossed up, the rough edges shaved off, a little simpler and smoother. The things I listed above really don't count as changes... they're just improvements on the old engine or, in some cases, taking a good idea from a previous edition and implementing it.
One bad change... the OGL. No one can write an adventure set anywhere but Foreven without permission?