my company attempted (and still attempting after years of trying) to do the same transition and so far personally, I haven't seen much success with it. During this transition, I did a whole lot of reading up on agile development and different ways/aspects/concerns/techniques and one thing I strongly agree with is that pure agile development is best suited when entire team consists of senior, high-quality people (or at least all people of the same level).
Last release I was on an "agile" team that had IMHO too many developers with skill levels all over the place and we attempted to get everyone involved in the same project. It was a disaster. We did more talking/arguing than work, and in the end what the team produced was an average work (read Peopleware or Mythical Man Month about taking average). Forget about design patterns, forget about low coupling or breaking code into small classes and methods. Forget about trying to make anything interesting because a) that couldn't be explained and understood by all team members (at least not in timely fashion) and b) since we were agile, whatever I started this iteration, someone else with absolutely no understanding would continue in the next iteration. Personally, I just gave up and simply waited for scrum or whoever to assign me tasks, did them, went home and coded my own personal projects.
I absolutely hated the fact that I couldn't do anything with C++ templates, or write some cool (but somewhat complex) low-level framework libraries which would have made our lives so much easier. How can something like that be done when no one else on the team is even capable of reading STL header files but we are all supposed to be working on one thing at a time. Entire project ended up being brute-forced feature by feature because that's what agile seems to emphasize.
At the same time, there are few (very few) people in my company that I would absolutely love to work with side by side and share all of my code.
But now you face a choice. A) Take all your good, senior developers who produce high-quality code and put them into their own team and put the rest into a separate team. Or B) attempt to balance out teams and put good ones with not so good ones. In (A) the problem is that one of your teams will be way underperforming and won't pick up good skills/habits from the good guys. In (B) your good guys (in pure agile environment) will feel frustrated and will start working on their resumes. Mine is up-to-date.
So what are you to do?
I do not know if this is the right solution. Ask me again in about a year or so. But what if instead of "pure agile" you formed a team, but clearly identified which person(s) has more influence (design, code reviews...) and make sure that person understands that and is rewarded for extra responsibility. As the team members start working together, identify those that are picking up good habits/practices and elevate them to the same level as your good people. Hopefully as people spend a release or two working together, they will learn what the other person thinking and how they work, so they'll be more compatible to work in the same code at the same time. But until that happens, if you just throw people into a project, it'll be nothing but frustration (again, just my opinion). This way if senior guys have to work with less experienced ones, at least they have more weight (not dictatorship, just more weight) in decision making.
Some of my thoughts are based on how I started professionally in software. When I was a co-op I worked with a guy who was my mentor. He taught me everything from coding ethics to good design to reading thousands upon thousands of lines of code you didn't write. In the beginning we were nowhere near on the same level and it would be laughable if we were placed in an agile team and told that we can work on each others code. But over time (few years), we started thinking very much alike. I could understand his code with a simple glance and he told me multiple times that he had absolutely no problems (and was suprised by that) navigating my code that he has never seen before. This took years, not something that happened over night. After experiencing disaster after disaster in agile environment in the last few years, I would jump in a heartbeat at the chance to work together with that guy in an agile team
This is not really an answer but it sums up my experience/observations. I do want to see what others would say about this.