The Doctor has many enemies, some iconic, some infamously corny, and few of them are threatening opponents in their own right. However, the Doctor is not a counterterrorism unit, he is a madman with a box. He stumbles into plans in the final stages of execution and, thus, much more difficult to stop. It is only with the help (manipulation) of those around him that the Doctor is so successful. In most cases, he is capable only of coming up with a solution that costs a life, which he means to be his. It is the awe that he inspires in others, prompting them to bite the bullet in his stead, that allows his track record. (See Silence in the Library, for exhibit A.)
In other cases, he faces an enemy that frightens him badly. For example, one Dalek ship, stranded and low on power, without the capacity to self-repair, pushes him to a frenzy, threatening to blow himself up along with their ship. His life in exchange for three Daleks.
Another example of someone capable of being called his equal is "The Master," another renegade Time Lord that consistently and effectively neutralizes the Doctor's strengths of intelligence, observation, and tinkering with technology. In those altercations, it nearly always falls to the companion to save the Doctor, rather than the other way around.
Doctor Who is a program about tension and drama, not mass/thrust ratios. Should the story and exploration of the characters be enhanced by facing difficulty, problems arise. Otherwise, someone knows the answer. The fun is seeing how a classic enemy will be implemented, and defeated, or watching the trainwreck that happens when the Doctor steps beyond his established limitations.
Spoiler:
One of the critical limits to time travel is that there are some events that cannot be altered. These "fixed points" in time are things to which the Doctor is sensitive. The episode Waters of Mars has him trying to rewrite one such event, but his actions lead to his own downfall, rather than any meaningful change.
Think character arcs, rather than power levels.