Yes, you should remove Akeeba CMS Update. The first batch of improvements we made are already integrated in Joomla! 3.5.1. The second batch of improvements we made to Joomla!'s own Joomla! Update (reinstall the latest version of Joomla!, install by uploading a package, upgrade from betas, proper handling of FTP when installing the update and I believe Hybrid FTP/Direct File Write mode) will be integrated in Joomla! 3.5.2. In the past we had already integrated choosing the update channel (long term support, short term support, testing etc) and improvements in the extraction engine and post-extraction update handling.
So, basically, after Joomla! 3.5.2 Joomla! Update will be in par with the feature set of CMS Update. That was the goal of CMS Update from the very beginning: it was a testing ground for new features we wanted to submit to Joomla! itself. After three long years it's finally mission accomplished!
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!