First of all, make sure that your sales process is super consistent and running smoothly. "Lead Status" should be used very consistently, because that is going to drive your model. Your model should be as simple as possible, transitions driven by changes in lead status. Usually, the model requires some optimization and debugging, so the simpler the better.
Hope that helps.
Alternatively, you can create yourself a custom status field on both the Lead and the Contact. This way, you can always see the current status of the lead in SFDC - regardless of whether it is a Lead or a Contact. I like to call this field "Lifecycle Status".
My models always follow the status changes in the Lifecycle Status. This keeps the logic simple in the models, and I can use Lifecycle Campaigns to manage the transitions and process other steps, such as Sync to CRM, Change Data Value of other fields, or reset scores as needed.
I agree with Jep that the model should be simple - you want to track the major milestone, not every task a salesperson performs, or every Opportunity Stage. Keep it high level - you want to be able to see how quickly leads are moveing, where they get stuck, and be able to segment your nurture activities based on the progress the lead has made in the model. If you want to get as granular as analyzing the sales process, you can always run a report in Salesforce.
Here is an example of a model I created:
MCL = Marketing Captured Lead
MEL = Marketing Engaged Lead
MQL = Marketing Qualified Lead
SAL = Sales Accepted Lead
SQL = Sales Qualifeid Lead
Not a Lead = Competitors, Employees, out of sales territorry, bad information, etc.
Note that there are many transitions to "SQL" - this is because sales can add a contact to an opportunity at anytime, regardless of where they are in the process - the Contact Role on the Opportunity doesn't have any restrictions. You want your model to accommodate this. On the other hand, there are no Contacts in MCL, MEL, or Not a Lead.
I recommend resetting the Behavior Score when a Lead goes into Recycle or Lost. Then keeping leads in Recycle until they reach the MQL scoring threshold again (instead of moving them to MEL as soon as they re-engage). This way, you don't skew your early stage transition metrics with a mix of new and recycled leads, and you can better track how your lead generation efforts result in MQLs.
Given that there are so many "moving parts" in the CRM that could influence how a lead progresses, it is a good idea to engage an experienced Marketo Consultant who has successfully built models before. We offer a 2-day workshop to discuss your process, design the model and implement the transition logic. We can help you test the process and assign your existing leads as well.