Since using Infusionsoft, the design of the Opportunities section has always been like that. Either people live with the design, or use some sort of workflow to get around the limitations, or use something else.
I have a product that I develop that adds features into Infusionsoft Interface. One of the recent requirements I had was to hide or rename the sub-sections within the Opportunity General Tab. That was due to a client wanting to hide things for their staff members. Not the same in your case, but it there is other people who want things done differently.
Your suggestions require changes within Infusionsoft in which I do not see happening. Not a lot has changed in the Opportunities section for a very long time. So I am thinking that a 3rd Party Service / Software would be the best way. If your requirements are critical, then you may have to offload the Opportunities to something else.
Have you considered something like a Project Management Tool? Something like Basecamp: https://basecamp.com/ or Teamwork: https://www.teamwork.com/ Those would track activity, do notes, tasks, etc.