While many have joined the bullish camp in recent weeks, several top strategists remain much less enthusiastic about stocks, notes TheStreet.com’s Stan Luxenberg.

Chief among the bears is Rob Arnott, of Research Affiliates and the PIMCO All Asset fund. Arnott, who recently published a paper saying that bonds — not stocks — have historically been the best investment vehicle, continues to see challenges to stocks. He’s been underweighting stocks and focusing on bonds.

Arnott is concerned that Washington’s recent actions have changed the rules of the financial markets, which will hurt stocks for years to come. Stock holders never used to worry that government interference would dilute the value of their holdings, Luxenberg says, but now, Arnott thinks the Obama administration looks ready to “stiff stock and bond holders” as banks and auto makers restructure.

“We need to recognize that centuries of contract law have far less meaning than in the past,” says Arnott, whose PIMCO fund has returned 3.7% per year over the past five years (through May 15), beating the S&P 500 by about 6 percentage points per year. “This means that assets must be priced lower, with higher yields, to compensate for this new layer of risk.”

Other managers are also focused on bonds. Louis Stanasolovich, president of Legend Financial Advisors, thinks stock returns won’t overtake bond returns for at least a decade. Taking the S&P 500’s historical earnings growth of 6% and its current dividend yield of 2.6%, the index could see annual returns of about 8.6% for a while. Corporate bonds, meanwhile, currently yield almost the same, Luxenberg writes.

Stanasolovich warns that stocks are still not cheap. In past bears, the S&P’s price/earnings ratio has fallen to 7, but it now sits around 12, he says, adding that huge debt levels could slow the economy and hurt stocks. “This is a time to underweight equities,” he says.

Another notable bear is the No-Load Fund Analyst newsletter. Its publisher, Litman/Gregory, “recently sounded a bearish note, arguing the S&P 500 would likely return less than 0.5% annually during the next five years”, writes Luxenberg.

High debt and unemployment will create an earnings decline nearly as steep as that of the Great Depression, Litman/Gregory thinks. The newsletter currently has 43.5% of assets in equities and 56.5% in fixed income, compared to a neutral weighting of 60% in stocks and 40% in bonds.