I got my first ever road bike earlier this summer, too, and had a lot of the same issues/discomforts. Now I like it more than my mountain bike! I still enjoy going biking on the trails and such, but it is SO nice to be able to go so fast without much effort. I ended up getting used to most of the things you listed above, but the only one that still bugs me a bit is not having the numbers on the gear changers.

The other day I rode my mountain bike around and actually felt awkward and uncomfortable on it compared to my road bike.