Mulally goes off bedecked with laurels, and he leaves Ford in the strongest competitive position it has enjoyed since the late Taurus/Explorer years of the 1990s. Somewhat miraculously, he revived the company and set it on a new strategic direction while also becoming the most popular CEO in Ford (F) history and the object of universally admiring media coverage. Unlike his sharp-elbowed predecessors, he governed with carrots instead of sticks.

But before we get too nostalgic about Mulally and the changes he wrought, it is important to remember that his tenure wasn’t all about attaboys. Corporations, auto companies especially, are complex entities, and there is more to the Mulally era than is immediately visible on the surface:

1. Mulally is unique

Mulally possessed a unique combination of competiveness and charm, leavened with a guilelessness that appeared to be rooted in his Kansas church-going, Eagle-Scout upbringing. Enthusiastic and fair-minded, he was able to push changes on Ford’s executive team without damaging fragile egos or igniting turf battles. It would be unfair to expect Mulally’s successors to duplicate his performance.

2. Fields is not Mulally

Fields is smart, hardworking, personable and knows the company and the industry inside and out. But some see him as slick and insincere, which will make it difficult for him to preserve Mulally’s kumbaya corporate culture. The additional fact that Fields is perceived as being close to executive chairman Bill Ford could also lead to a revival of Ford’s palace politics that in years past has resembled an episode of Game of Thrones.

3. Strategic issues remain unresolved

Mulally’s One Ford vision of One Team/One Plan/One Goal sought to unify the company’s operations around the world. Yet Ford remains a North American-centric automaker that gets the bulk of its profits from the truck business. In 2013, it made $8.781 billion in pre-tax profit on auto operations in North America and lost $1.228 billion everywhere else. Ford’s best-selling vehicle, the F-150 pickup, is a non-starter in overseas markets.

4. Foreign operations need more work

Ford is making up ground in China where it has long lagged, and Automotive News reports that it has passed Toyota (TM) in sales. It now ranks fifth among Western automakers, though way behind Volkswagen and General Motors (GM). A new product blitz is boosting sales in Europe, but the region remains a money loser. Ford hopes to trim losses this year and return to European profitability in 2015.

5. The Lincoln brand is still under construction

As a man whose wardrobe seems to consist of a blazer, slacks, and a single red tie, Mulally never seemed comfortable with the upscale car business, and Lincoln is still in the early stages of a rebuilding process that even division executives say will take 20 years. With competition fierce in the volume car business, a robust premium line is key to improved profits, but Lincoln provided little in the way of margin expansion during Mulally’s tenure.

6. Selling Jaguar and Land Rover was a mistake

Early in his tenure, Mulally sold Jaguar and Land Rover to Tata Motors for $2.3 billion so he could focus on Ford brand cars and trucks. Although he continues to defend the decision, Ford shareholders wish he hadn’t. After investing in new models, Tata has now recouped its purchase price several times over, while Ford has two fewer opportunities to command premium prices for its products. Jaguar and Land Rover may have been distractions at the time, but there was clearly unused leverage in their heritage and reputation.

7. Ford has its own culture problems

GM has been justly roasted for its belated recall of faulty ignition switch cars. But Ford has now been twice found guilty of inflating the window-sticker fuel economy ratings on a half dozen of its models by as much as seven miles per gallon. All of the cars involved were either small cars or hybrids whose appeal rests on their ability to achieve high mileage. Although Ford apologized and said it would compensate owners, no Ford employee has been publicly held responsible.

8. Ford has turned on the money spigots

Working at Ford has made Mulally a very wealthy man. He made $23.2 million in 2013–a big number for the slow-growth auto industry–and holds about $100 million in Ford stock. Ford also picked up his tab for $93,275 in housing and living expenses (Mulally lives in a company-owned house) and $232,153 for personal use of private aircraft.

The second highest-paid executive at Ford these days isn’t Fields but Bill Ford, who also holds down a part-time job as vice chairman of the Detroit Lions, His total compensation in 2013 was $11,955,820, some $1.8 million more than Fields’ $10.2 million. Ford’s pay package included $1.4 million in perquisites: $275,639 for personal use of private aircraft and an eye-popping $912,151 for security.

9. Timing is everything

It takes nothing away from Mulally’s record to point out that he benefited from better-than-average timing. He took over two years before Lehman Brothers’ collapse and after presciently raising $23.6 billion for a rainy day fund, steered Ford through the deep global recession that followed. Then, as the economy recovered, he rode the revival of auto sales back up.

It is a run similar to that of Jack Welch, who took over General Electric in the middle of the early 1980s recession and retired as the economy was peaking. Welch’s successor Jeffrey Immelt has had a difficult time duplicating that performance. Likewise, Mark Fields takes over when auto sales are near a cyclical peak. So it seems sensible to fully grade the Mulally record as CEO with an incomplete until the economy goes through another valley. The impact he made with his personality, style, and leadership, however can already be measured as historic.