I can understand why people may have doubts in the system. The modern day mind is very skeptical, and want scientific proof for everything that they are presented. In a way, perhaps, it is good that people want to check things out and not accept things on blind faith. (There is a fine line between wanting to check things out and question for the purposes of learning, and wanting to question just for the sake of being argumentative, which can become very disrespectful)
This is also why the tulku system isn't something that is arbitrarily decided on but also follows a very systematic way of checking. Normally, a tulku is not identified just by one random person but undergoes a series of very stringent "tests", and his status is questioned, checked and ascertained by divination done only by the highest masters.
I think the surest sign of the fact that tulkus exist is by the actions of each lifetime itself. They don't need to be identified and recognised to continue doing great things in "this" life. Often, their actions eventually begin to match everything they were known to have accomplished in their previous lives and they continue to benefit others in everything that they do. Many tulkus, in fact, are so humble as to not even talk about the fact that they are tulkus. Often, they will deny remembering anything of their previous lives. Instead, they concentrate on the present life, they will often tell you that it is more important to focus on what they are doing right now. And sure enough, what they are doing right now mirrors (or exceeds) what they were doing in previous lives. To me this signals that, whether tulku or not, these are very great beings indeed.