When the first SMART train rolls down the tracks three years from now, Lillian Hames should have a seat in the front. She deserves it.

As general manager of the Sonoma-Marin Area Rail Transit District for the past 10 years, she has served the region and the nascent rail system well. She has taken the train system far — from a ballot argument to a construction project.

But Hames was not to be the person to take it all the way. This was becoming evident before Friday, when Hames suddenly resigned amid ongoing debate about the rail system's financial challenges and the necessity to build a truncated rail line — something far short of the 70-mile Cloverdale-to-Larkspur line that voters were expecting for when they approved funding for the system in 2008.

We don't know all the issues that led to Hames' resignation, but there's no hiding the fact that the transit system has been a focal point of controversy this past year.

In fairness, SMART's biggest problems were not of the general manager's making. A reeling economy was dealing the rail system a major financial blow before the votes were counted in November 2008.

Nevertheless, SMART was slow to give voters a clear accounting of the transit system's funding woes in the ensuring months. And when it finally showed its bottom line — a shortfall of some $350 million — the organization responded with a plan last year that can only be described as politically clumsy.

A tentative plan, which called for SMART to build the first phase from Larkspur to Sonoma County in hopes of using that idea as leverage to get federal funds for the Santa Rosa phase, backfired. It was a long shot that failed and, in the end, hurt the system's credibility.

The system took more heat later in the year when it issued another phased plan that called for building the system from Santa Rosa to the Marin Civic Center. This earned the ire of those in Marin County who ultimately were appeased only when SMART directors agreed to extend the system to San Rafael.

While we don't hold Hames personally responsible for all of these gaffes, her departure creates an opportunity to begin anew — to establish some new leadership that will oversee the completion of the project.

SMART's new chairman, Sonoma County Supervisor Valerie Brown, said she expects a new general manager will be hired within 30 to 60 days. We encourage the SMART board to take its time. Given SMART's recent challenges, it's more important to find the right person than to adhere to a time line.

With SMART on the verge of starting construction, the rail system needs the leadership of someone who can build political relationships and community partnerships, pursue new funding sources and maintain transparency — all while building a $400 million commuter train system on a tight budget.

Finding the right person will be challenging. But it will be the most important decision the SMART board makes this year.