You are confused.

First, The election in which the Supreme Court intervened was the 2000 election. George W. Bush had not been president for a nano-second at that point and could not have appointed any Justices. Bill Clinton had been president for 8 years; he appointed some two of the Justices that were on the court in 2000. George H. W. Bush also appointed two. The remaining Justices had been appointed by earlier presidents. If I am not mistaken, George H.W. Bush and Bill Clinton both appointed Justices who were confirmed by a Senate in which the majority party was Democrat.

Second,
The electoral college system is what provided the environment for the elected president to have fewer popular votes than his opponent - yet still win the election. This system was in place decades before George W. Bush was even born. Read a little about the electoral vote system and attempt to understand how it works. You may find that it is a good thing.

Third,
There were indeed reports of problems with voter fraud in the 2000 election; none of the allegations that I know of ever really amounted to much in real terms.

If you want to learn what really happens in the election business, work - not in a campaign - but rather in the elections business. Take a job with one of the voting equipment vendors, the election office in your county or state, or be a poll worker. What you will likely find is that these people are dedicated to their task and work hard to produce a good result. These folks vote, like you, for the candidate of their choice. At the end of the day, though, they are less concerned with who wins than with how the election was conducted and concluded.