I’ve never understood the plethora of fanfics that make Kaoru and Tomoe out to be mortal enemies, battling each other for supremacy in Kenshin’s heart. They were both good for Kenshin at the times he met them. He met Tomoe when he was swirling in chaos and at the brink of insanity from all the killings he had done. Tomoe was quiet, refined, feminine, the paragon of Tokugawa Era womanhood. She questioned him and made him question what he was doing. She broke through the fog and led him back to the light of sanity again. I shudder to think of what Kenshin would have turned into if he hadn't met Tomoe.
Even her death, as painful as it was for him, was necessary. She taught him what it's like to lose a loved one. Kenshin was so young when his parents died, he might not have a clear memory of what that was like. He only knew the three girls who cared for him as a slave for one day, not a long enough time to form a close bond with them. Tomoe was the first person who really got close to his heart and that he really loved. So when she died and it wounded his heart, that taught him the lesson of what he had been taking from other people whose loved ones he assassinated.
Fast forward 15 years. Kenshin is a man of nearly 30 years. He's spent the last ten years wandering Japan, helping people, likely fighting and avoiding killing. Now, he meets Kamiya Kaoru. She's fiery tempered, willful, loud; the exact opposite of Tomoe. Though he is hesitant, Kenshin finds himself growing closer and closer to Kaoru as they live together. He brings her something she has been bereft of since her father's death: companionship. He helps her put her school back together by bringing Yahiko to her. They meet Sano and Megumi, whom he convinces to turn from the destructive paths they are on. Together those five form a tight-knit little family group.
After this, Kenshin once again found himself getting closer to people. He and Kaoru had growing feelings for each other, though he likely tried to convince himself he didn't, fearful of a repeat of what had happened with Tomoe. He found himself developing friendships with Sano, Yahiko and Megumi as well. These were things that he hadn't been able to permit himself since the loss of Tomoe.
When Kenshin left for Kyoto, Kaoru, Yahiko and Sano followed him. This was probably the first time someone had followed him after he left a place he had been staying at. They fought at his side and helped him to defeat Shishio. Then they all went home together. For the first time, Kenshin realized that he had people around him who cared about him. Not just people who were nice to him for a while and then sent him on his way again.
Then the Jinchuu happened. Enishi took Kaoru, leaving Gein's horrible doll in her place. Kenshin thought her dead, a repeat of Tomoe, and had a nervous breakdown. Calls for revenge from Sano, Yahiko and Misao went unanswered as he rotted in Rakuninmura. The only thing that woke him up again was when Tsubame told him that Yahiko was going to be killed by the berserker Kujurinami.
In the aftermath of the fight, Kenshin dreamed of Tomoe, who told him that Kaoru was alive and being held on an island by Enishi. She told Kenshin to go get Kaoru and be happy with her. She released him from the guilt and penance he had been suffering for the last 15 years. Finally, Kenshin was a wanderer no more, but rather a man going to claim his woman from the man who took her from him.
After that, the whole group went to the island, fought and ultimately saved Kaoru. Kenshin was finally able to love Kaoru without reservation because Tomoe released him from his guilt. Kaoru showed him how to live and love anew. Thus the healing that began in Tomoe was completed in Kaoru.
Though Tomoe and Kaoru seem like polar opposites at first glance, they're really not all that different from each other. Both wanted Kenshin to be happy and live his life to the fullest. Tomoe taught him the value of human life and Kaoru showed him the value of happiness and that he could rely on others and not always carry others on his shoulders.
Some people say that Tomoe was better for Kenshin because Kaoru only loved him as the Rurouni and couldn't accept him as Battousai. What these people fail to understand is that Kaoru does fully love Kenshin, both sides of him. The reason she hates when he becomes Battousai is that if he were to kill someone in that state, it would shatter him and he would leave her to wander again, a broken man, never to draw close to anyone again.
Some say that Kaoru is better because Tomoe didn't love him at all and was really out to kill him. While it's true that that was her original intent, I'm fully convinced that by the time they fled to Otsu, she was beginning to fall in love with him. Certainly, she couldn't love him fully and without reservation because of her feelings for Kiyosato, but she did love him. She saw that he was really a frail young man who had been turned into a mass murderer by the Ishin Shishi. At the critical moment, she threw herself in between him and his foe to shield him. She knew she was going to die and was glad to do it so he could live.
In conclusion, both Tomoe and Kaoru loved him, albeit in different ways. Both were good for him for the place in his life he was in at the time. One to rescue him from the brink of insanity and the other to teach him how to live and love again.