Are Scalia and Thomas upset that they were not appointed to Chief
Justice of the Supreme Court, and instead Roberts, a newbie, was
selected?

Based on the clear language of the Constitution, what was the worst
Supreme Court decision that has not yet been overturned, and will
Chief Justice Roberts be able to overturn it?

As to the second part of your question, United States v. Miller, a decision
on the Second Amendment, is easily one of the worst decisions.
http://caselaw.lp.findlaw.com/data/constitution/amendment02/

No, if John Roberts Jr. is appointed to the Supreme Court, he would not be
able to overturn it, even if the Supreme Court did operate as such, which
it doesn't.

Wait a minute...

they made the right call there.  How would you interpret that amendment?

The beginning of the 2nd Amendment:

"A well regulated Militia, being necessary to the security of a free
State, ..."

Clearly states one reason, but not all of the reasons, for the rest
of the amendment:

"... the right of the people to keep and bear Arms, shall not be
infringed."

Note that the second part does not state anything such as "only
members of a Militia can keep and bear Arms" or "Congress can
regulate Arms" or "the right of the Militia to keep and bear
Arms" or any restrictions at all.  The meaning of the phrase "shall
not be infringed" is clear as well.

The intent of the 2nd Amendment is clear.  If it wasn't, why hasn't
Congress just outright outlawed civilian (read: the people) ownership
of arms?  Why didn't the Supreme Court, as part of that decision, go
ahead and restrict arms ownership to the "militia" at the time, if
that was the clear intent of the amendment?

Because it would be unconstitutional, and the Congress and the Supreme
Court knew that it would be unconstitutional.

At pure face value the decision is incorrect as well, as sawed off
shotguns have been used with great effectiveness in military and
resistance (read: militia) operations in several wars and conflicts.

The Supreme Court makes mistakes.  The ability to parse a relatively
simple English sentence was one of them.

Sometimes when they say "the people" they're talking about State's
rights, vs. Federal Law.  So maybe the Federal government can't
overrule the State government on gun laws.

The founding fathers certainly lacked foresight when they came up with
the second amendment.

As to your first question, it would be hard to speculate on the
emotions of existing justices.  However, Rehnquist was only the 5th of
16 Chief Justices to be elevated from the bench.  Bringing in an
outsider as Chief Justice is historically common.

Here is the ABA's view on Unites States v. Miller and the Second Amedment:

"Second Amendment Issues"
American Bar Association
http://www.abanet.org/gunviol/secondamend.html

Of course, there are many more opinions about Miller, some positive,
and some negative like denco's.

For am in depth analysis on "United States v. Miller," there is this
paper that originated in the "Cumberland Law Review."
http://www.guncite.com/journals/dencite.html

"CAN THE SIMPLE CITE BE TRUSTED?: LOWER COURT INTERPRETATIONS OF UNITED
STATES V. MILLER AND THE SECOND AMENDMENT" by Brannon P. Denning.

So I guess everybody thinks Roe v. Wade was okay?

The Miller decision was actually a model of judicial restraint.  It
did not pronounce on the issue of collective versus individual right. 
It merely said that a sawed-off shotgun either wasn't a militia
weapon, or should be determined by further proceedings at the district
level  --  on that question it is ambiguous.