1.    The Michigan primary was not a sanctioned by the party.

Michigan sets an unsanctioned primary day. In response the party penalizes Michigan by decertifing its delegation. Obama and Edwards remove their their names from the ballot after being given assurance from the party that the primary won't count. The result is Obama's name was not on the ballot, and Hillary Clinton picked up 328,309 popular votes.

If the same procedures were used in some third world election, no one would call it fair. No one but a Clinton supporter would consider the Michigan primary as a fair measure of the will of the Michigan voters. Many of the same arguments apply to Florida but to a lesser degree as Obama and Edwards were both included on the ballot.

2.  Votes cast at a caucus and votes cast at a primary are not comparable.

States are awarded delegates based on their population and percentage of Democratic voters in the last to presidential election. The bigger your state is and the more people who voted Democratic the more delegated your state gets.

The party leaves it up to each of the states as to how to divide the delegates between candidates within certain rules. Some of those rules include prohibition of winner take all primaries and rules for how delegates are awarded to candidates. Many things are left to the state party to decide such as whether or not the primary will allow voters from outside the party, whether or not to allow registered Republicans to vote in Democratic primaries and whether or not to hold a primary or a caucus.

States chose to have caucuses instead of primaries to save money. Elections are expensive and most years small states don't have much influence over the selection process. That is why many states chose caucuses. Caucuses require fewer locations, fewer poll workers and counters and they have limited hours. As a result they get a much smaller turn out. Caucuses require more of the participant and cost the party less.  Caucuses get lower turn outs because they are designed to get a lower turn out not because of voter apathy.

Suppose there were only two states in the nomination process, Rhode Island and Hawaii. Both states are about the same size and have equal weight in the nomination process.

Hawaii has 20 delegates and Rhode Island has 21 delegates. Hawaii has a caucus and Rhode Island has a primary.

In Hawaii 37,282 Democrats participated in the caucus.  28,347 (76.1%) of them chose Obama. 8,835 (23.7%) chose Hillary Clinton. Obama got over three times as many votes and was awarded 14 of Hawaii's 20 delegates, Hillary got 6 delegates.

Rhode Island has a primary and 183,465 voters turn out. Obama gets 75,316 (40.4%) votes to Hillary's 108,949 (58.4%). Obama gets 8 delegates and Hillary gets 13 delegates.

Total up the delegates and Obama has 22 delegates and Hillary has 19 delegates. Given that Obama won one contest by 53 points and lost another contest by 18 points and both contests were about the same size that seems roughly fair.

Now total up the popular votes, Hillary has 117,784 votes and Obama has 103,663 votes. Look Hillary has the lead even though Hillary lost one contest by 50 points and won the other contest by 18 points. Both states are about the same size. Judged by the popular vote it seems that Hillary has more support from the party. Under this system Rhode Island has 2 times the impact on the race as Hawaii. Is that fair? Should Hillary win just because the contest she won happened to be a caucus?

See it is unfair to count votes from caucus states as if they were primary votes. If all states had primaries then the popular vote might be a valid measure of party will. If all states had caucuses then popular vote might be a valid measure of party will. But as it stands mixing votes from primaries and caucuses as if they were the same only results in meaningless distortion.

Obama did not decide which states would be primary states and which states would be caucus states. There were 11 states that held caucuses (Iowa, Nevada. Idaho, North Dakota, Kansas, Nebraska, Hawaii, Colorado, Washington, Minnesota, Alaska, Wyoming, and Maine) Obama won 10 of them. The caucus states awarded 347 delegates. Obama won the caucuses by an average of 40 points and Obama received 224 delegates to Hillary's 115 delegates, yet Obama only gained 280,000 "popular votes." Hillary won Kentucky which has 50 delegates by a 30 point margin and gains 249,000 popular votes. So in one primary Hillary erases nearly all of Obama's margin in popular votes in 11 contests even though Obama had won 10 of those contests by a greater percentage margin and the 11 caucuses were awarded 5.5 times as many delegates.

The net effect of counting caucus votes as if they are primary votes is the diminishment of importance of caucuses by about 80%, even though caucuses are fully sanctioned by party rules. In effect Hillary wants to discount the votes of the 11 states which chose to have caucuses by 80%, how fair is that?

In summary:

Hillary does not have the popular vote lead unless you count Michigan as a fair primary. Even if you counted Michigan as a fair primary it would not be legitimate to count the popular vote as a measure of party will because caucuses are designed to get a much smaller turn out.

If Hillary wants to argue that the party was all wrong and picked the wrong candidate she is free to do so. But is she wants to argue that she is really the one who the rank and file party members chose as witnessed by the popular vote the she is playing fast and loose with the facts because you can't honestly say that Michigan was fair election and even if you could you can't count the votes from caucus states as if they were primary states and get an accurate reading on the will of the party.