Short answer:

Since the day they went to the polls on Nov. 7, Floridians' votes have been treated differently depending upon the county in which they live.  This varying treatment was caused by the different voting systems used across the state, the different ways counties reacted to the automatic recount, the different ways votes were counted during manual recounts, and the different ways absentee ballots were counted.  If Florida's manual counting standards violate the constitutions equal protection standard, then Florida's entire vote count, along with numerous other states, is unconstitutional.
 

Long answer:

Bush lawyers have argued that the statutory standard for manual counting will be applied across different counties leading to a violation of the constitution's equal protection standard, which insures that everyone's vote will be treated the same.  The reason the Bush camp claims that the manual canvassing standards will vary across counties is because the standard set forth by Florida Law for counting such ballots is as follows:  "No vote shall be declared invalid or void if there is a clear indication of the intent of the voter..." Section 101.5614(5).

However, this concern over equal protection is a bit late in the game.  Bush's allegation assumes that the current vote tally in Florida is not already in violation of this equal protection standard.  Unfortunately, that is not the case. Florida's vote tally, and probably numerous others around the country, represent a gross violation of this standard.

Here is the case for why voters and their ballots have been treated differently in different counties since Election Day:

1) Variability in the Voting Systems
On Election Day, voters in different counties cast their votes on different voting systems.  Voters who voted on the punch card system were 2 to 4 times more likely to have their ballot rejected by machines then those voting on more sophisticated optical scanning systems.  As it turns out, the system through which more than 60% of the votes were cast, the infamous punch card system, accounted for more than 80% of all the uncountable ballots (uncountable by machine anyway).  The average number of rejected or spoiled ballots from these counties was roughly 5%.  Gore handily won the majority of votes cast on these ballots.  The system through which about 35% of Floridians cast their votes, scan ballots read at the precinct, accounted for only 10% of all the uncountable ballots (uncountable by machine anyway).  Bush won the majority of votes cast on this highly accurate system, which had an average county "lost vote" rate of roughly 1%..

Bottom line: This first count violated the equal protection standard because voters and their votes were treated differently depending upon the county in which they cast their vote.

2) Variability in the First Recount
An automatic recount was required under Florida Law due to the closeness of the results on Nov. 8.  However, at least 16 counties did not actually do any recounting.  This lack of a recount contradicts even Secretary of Harris' 1999 legal opinion issued to Manatee County in which she claimed that a recount means to count the ballots again.  While it is hard to determine exactly what the other 61 counties did, as many as 10 definitely ran every ballot back through their machines -- a total of about 2 million ballots containing a majority of votes for Gore (about 57%).  These rescans turned up roughly 1,700 vote changes
(either new votes for a candidate or removal of votes).  What many people don’t seem to realize is that 10 more counties went beyond rescanning every ballot and included manual recounts of ballots the machine would not read.  Thus, roughly 800,000 ballots (a slight majority of which favored Bush) were put through a recounting process that included manual inspections.  These recounts turned up about the same number of vote changes (1,800), as the rescan-only counties despite processing half as many ballots.  Considering all the whining about the unfairness and subjectivity of hand counts from Republicans, it may surprise you to know that seven of those counties favored the GOP candidate.

Even more amazing is the variation in the standards used to determine the “will of the voter” during these manual inspections in these counties.  However, this is the standard set forth by Florida Law.  Some counted ballots with double votes on them if the voter clearly indicated his or her preference by circling a candidate’s name or listing that candidate in the write-in box.  Other counties disqualified these votes, only counting those with marks in one circle unreadable by the machine because they were too light or not filled in all the way.

Bottom line: the automatic recount violated the equal protection standard because voters and their votes were treated differently depending upon the county in which they cast their vote
 

3) Variability in Counting the Absentee Ballots

Florida law has strict standards for what constitutes an acceptable absentee ballot.  One of those requires that they must bear a
postmark, presumably so officials can tell if they were sent after Election Day.  However, Florida’s Secretary of State sent out
a memorandum on Nov. 13 to every county outlining the standards to be followed during the absentee ballot counting in which
she affirmed the need for a postmark but added that “they do not have to be postmarked on or prior to last Tuesday.”  Some
counties followed this latter guideline and accepted any postmarked ballot regardless of the date; others ignored it and
rejected ballots with postmarks dated after Nov. 8; still others decided to ignore the Secretary’s orders and Florida law
altogether by accepting ballots without postmarks.

The New York Times reported their findings from election officials regarding the absentee counting mess. Speaking in reference to Harris's instructions, “county officials said that was a reversal of past practice, in which ballots postmarked after the election were thrown out, and some complained that when they sought clarification, Ms. Harris's office gave them contradictory instructions….. In heavily Republican counties, county canvassing boards reviewing the ballots on Friday often decided to include military ballots that had no postmarks. In mostly Democratic counties, canvassing boards tended to throw out those
ballots.” http://www.nytimes.com/2000/11/19/politics/19OVER.html?pagewanted=2

In another article, the New York Times reports that  "Counties applied vastly different standards in deciding whether to throw out ballots."  It also contends that "election officials in several counties, however, said today that they had always understood that ballots postmarked after Election Day were invalid, and that they had rejected such ballots in previous elections…..But in several other  counties, officials took Ms. Harris's directives to mean that votes  could be accepted with no postmark at all, and  some said that they had been advised as much by her office over the phone.”  The go one to quote a county official who quipped "We've never done it that way before, so we're a little confused about that, but that's what they've told us," said  Stephanie Thomas, assistant supervisor of elections in Clay County.  htttp://www.nytimes.com/2000/11/18/politics/18OVER.html

Bottom line:  The counting of absentee ballots violated the equal protection standard because absentee voters and their votes were treated differently depending upon the county in which they cast their vote.

4) Variability in the manual recounts
As everyone should know by now, 3 Democrat leaning counties completed full manual recounts of all their ballots: Volusia, Palm Beach, and Broward. However, during this counting, each county's canvassing board applied the statutory "intent of the voter" standard.  However, the discretionary power inherent in this statute lead each county to count disputed ballots differently.  Palm Beach applied a very rigid standard while Broward applied a more liberal standard.

Bottom line: The manual counting of all ballots in only four counties violated the equal protection standard because voters and their votes were treated differently depending upon the county in which they cast their vote.

I could go on, but I think you should get the idea by now.  If Bush is going to argue that the equal protection standard is the paramount concern here, then they must argue that all of Florida's votes be disqualified because the state has yet to produce a certified result that was not achieved through gross variability in the application of Florida's election law standards.