It took me a while to like Matt Smith as well, but I've ended up liking him just as much as Tennant.
As for companions, same sort of thing for Amy. She's my favorite of all the companions so far even though I started off not liking her much for the first couple episodes; I feel like she gets much better after episode 7, Amy's Choice. As for the others, my order of preference goes Rose as second best, then Donna third, and then Martha in last place because she's awful compared to the others.
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