He did use his Solar Flare to blind Goku briefly in gt, which is the one time we have seen him go in for an absorption post Perfect form. Yes, his Regenerationn can probably be overtaxed, but it's still an advantage. I know that there are a lot of things we haven't seen him do mid combat, but that can be summed up as PIS, the plot requiring him to not use these abilities in certain situations otherwise he'd win. He could have blinded Vegeta with the Solar Flare before trying to absorb him in his second form, but he never did. The thing is, thanks to his Regenerationn and stamina, as well as Chrysalis's problems with getting around them, this match should go on for quite a while, allowing Cell to try different tactics. Most of his fights weren't long enough for him to use all of his moves.
I know that most of what I have listed are small advantages, but that's a LOT of small advantages. Chrysalis probably has bigger advantages, but he has more small advantages over her than she has bigger advantages over him. I know there's the "quality vs quantity" argument, so I'm not denying she could give him trouble. What seals it for me though is his versatility. Cell has a lot more abilities than her, and a lot more options. For example, he could potentially just destroy the planet like he tried to do with his Solar Kamehameha. Chrysalis can't survive in space as far as we know. Not saying he WOULD do that, but it is an option. Chrysalis also doesn't know about his Regenerationn, so she could potentially blow him up with her magic, only for him to come back stronger than before.
What about intelligence? who do you think is smarter/ a better stratigest?