Some quick context: The dive centers bringing people to Nusa Penida all work under the SOP—send a car/mini bus to the hotel to pick you up in` the early morning, drive to their fast boat in Sanur Harbor, wait for all the other customers, finally get going, do your dives, return to the harbor, and car/mini bus back to the hotels in the late afternoon. The vast majority of the divers will be pretty inexperienced and only dive for a day or two during their trip to Bali. Anyone coming to Bali to really dive will be staying on site in Padang Bai, Tulamben, Nusa Penida, etc... Of course, there is nothing wrong with all that, but I think one needs to go into Sanur diving knowing the situation.
That being said, I would absolutely book with Two-Fish, as they have the experience and resources to ensure that more advanced divers are not left to their own devices and are not considered an afterthought. They are big players in the Indonesian scuba world and have been around forever. For a one-off day of diving in touristy Bali, they are a solid choice. They are good people, and whenever I use them, everything is just fine.