The former Ferrari and McLaren driver helped negotiate Nico Rosberg's lucrative new contract earlier this year, but the German quit F1 as soon as he won the 2016 title.
Now, it appears that Mercedes have negotiated a complex contract release with Williams so that Valtteri Bottas can replace Rosberg.
However, Berger told Germany's Auto Motor und Sport: "I would have taken Wehrlein. Because it would underline your [driver] programme.
"Wehrlein gave a convincing impression in the programme, but he can only show how good he really is in a top car."
However, Berger said that he understands Mercedes's reasoning.
"Compared to Bottas, Wehrlein is certainly a risk. But perhaps the most clever solution is not always the obvious one," he said.
"I rate Bottas highly. He is fast, a good team player, a nice guy and he has earned the chance to prove himself. On the other hand, he did not stand out from Massa enough to say clearly 'He is the right choice'."
Berger also thinks that Mercedes's 2017 solution is only an "interim" one.
"Mercedes needs to think about the future regarding its drivers, because even [Lewis] Hamilton's contract will expire. They need an interim solution with a view to 2018," he said.
"The most important thing now is to find a second driver so that Hamilton doesn't fall asleep. But it could also be that without Nico, Lewis finds the peace he needs and doesn't get himself into trouble.
"I believe Mercedes will again be the benchmark in 2017."
The new season begins with the Australian Grand Prix on March 26.