There is no right or wrong answer when determining fantasy scoring settings. The biggest issue is what kind of impact you want the scoring system to have. As you may know, in standard leagues passing TDs are only 4 points while rushing TDs are 6. Part of the reason for this is to help equalize the QB and RB positions. It's also why QBs get 1 point per 25 passing yards while RB get 1 point her 10 rushing yards. QBs put up a lot more yards and TDs on average than RBs.
That's not to say that the goal is to make QBs and RBs totally equal (because they're still not even with those changes), but it closes the gap a bit. With increases point totals for QBs, it makes that position more important. For example, even a small change to 6 points per passing TD changes the dynamic of QBs in the league pretty dramatically. It also begins to separate QBs even more so that the elite guys like Brees, Brady, Rodgers and Manning outscore lesser options like Ryan, Romo, Schaub and Dalton. Those first four have lead the league in passing TDs for the past 3 years in a row. So, the more points a QB can score for each stat, the wider the range is going to be between the best QBs and the worst.
So, it really depends on what kind of dynamic you want for your league. Do you want QBs to dominate the point totals, and be the first picks in the draft? If so, then beef up their point totals. If you would rather not have them have as much impact on winning and losing, then go with the standard league setup, or even consider lowering their point totals if you really want to bring their value totally even with RB. This is where PPR has an advantage, as it gives a boost to RB and WR (especially WR, making them more consistent options) and makes them almost as valuable as a QB.