My top three would be:
1) Scrap the "Defence Team" thingy: I am sorry, but I have never, ever felt that the civil servants from the Department were on my team. On top of that, its not their job to defend Canada: its the people in uniform's job. So get all the people in uniform in Ottawa, and get them to work at a Headquarter under titles and job descriptions that are military (such as S.O. or S.S.O. strategy, plans, policy, intelligence, etc.) - and put all the civil servants in another building with the Deputy Minister and let them do civilian things (such as audits, contract management, historical records, statistics, etc.). When we had the Somalia Inquiry Show, It amazed me that not a single journalist wondered why people in uniform that appeared before the Commission were in Assistant-deputy Ministers' position. This point here also means that we have to scrap the ridiculous idea of always having to establish a correspondence in "rank", pay, benefits, etc. between the uniformed personnel and the civilians - which led to a huge bloating and inflation of higher ranking officers (particularly generals) not needed from a military point of view.
2) Scrap unified Basic: Give everyone a common set of minimal general military knowledge required of all in uniform and then let each element provide its own appropriate supplement to it and freedom to administer such basic training as they see fit. The requirements of the various elements are too diverse for a single basic as we have now: The army, where every officer is as much a soldier as the soldiers he leads, needs more stringent leadership, self-discipline and physical training which is easier to incorporate from the start at the regiment level (plus you can indoctrinate into regimental aspects right away, which makes you deployable to places like the sandbox much faster); The Air force, where officers do not lead others into combat except other pilots and the crewman are usually techs that work for the warrant officers, would probably be satisfied with the minimal requirements so that the techs get to the shop soonest with the minimal baggage needed to avoid military "faux pas" and insist more, in the officers, on training that instil probity and moral courage; Finally, the Navy, where the officers need to lead within the confinement of a ship people that have better and more thorough knowledge of their trade than the officer ever will , needs a basic course that introduces its people to the harsh environment of the sea and the personal skills relating to the close quarter living on ships from the beginning.
3) Institute a military wide "General Staff" corpus of officers, European continental style. This would be composed of officers identified early on for their strong intellectual capacities, processed through leadership positions a little faster early in their careers so they could then attend advanced military studies before reporting to headquarters where they would be the ones working on plans, strategy, long term planning and doctrine, before returning to senior field commanders headquarters to serve as their chiefs of staffs or similarly senior positions - providing these field commanders, strong in tactics and logistics, with the strategic thinking and detailed knowledge of national plans. Such a corps would provide the CDS with a corporate memory he currently lacks, which would make him much more capable, regardless of personal career history, of providing properly thought through military advice to the civil leadership (the PM).
Just my thoughts.