1. Yes, season 4 got "darker." Not just because of Black Mask. Most of episodes in season 4 are closer in tone to B:TAS; closer but not the same by any means. Some really great eps are "A Matter of Family," "Strange New World," and "Artifacts".
2. No Ra's yet. I believe he and Scarecrow have been under the "Bat Embargo" imposed by the WB film division.
3. Defining Joker as a loser is a subjective analysis, I don't really remember too much about his 1st season appearance other than the 2 part finale, but "The Laughing Bat" from season 2 and "Two of a Kind" from season 4 are pretty good Joker eps.
4. The Kabuki Twins continue to appear frequently with Penguin all the way through season 4 episodes.
I think many on the boards will agree the Season 1 of The Batman, is not representative of future seasons. The creative team really turned out some quality stuff in season 2, and season 4 is filled with gold. Season 3 is a matter of taste, some hate it some love it. I didn't have any major problems with it. But they definetly ramped it up in season 4. Hopefully the quality will stay up there during season 5.