I'm guessing you just mean the first time over? Because I've made different choices in subsequent files...
Anyway:
-Didn't find all of the police officers before battling Taka/ZEL... in my defense I had no idea where the last one was. (I did indeed go back and find him later, though.)
-Lost to the Garchomp, although now I'm wishing I'd worked out a strategy to defeat it back then, now that I know it's possible...
-Fought Sigmund in the Yureyu Building, and Sirius in Tanzan Cove.
-Chose to stay downstairs, rather than following Sigmund upstairs after that. (Incidentally, this leads to Anna and Noel being kidnapped.)
-Hahahahaha is this a trick question? No? I like Radomus' character too much not to side with him, difficulty or no. Ditto-ceus can't handle Gengar's Destiny Bond, anyhow.
I was more lax about what I did in my main file, since that was the first time I'd been thrown into these situations and wasn't sure what effect my choices would have later on. Still going to be more lax about it for any future situations like these, I think.