The functioning of the patent system is broken in many ways.
Examiners don't understand software; they have no backgroung in
software; they are not paid enough to attract capable software
developers.  There is no way to classify these patents, so that
sometimes two patents are issued for the same technique.  The standard
of unobviousness is absurdly low in all fields.  Patents can issue
decades after the original application, and there is no way ever to be
sure a technique will not be covered by a patent issued next year.

Therefore, there are many ways that the patent system could be made to
function better, at least in principle.  These reforms would be an
improvement, because they would reduce the number of patents which
might subsequently hamper software development.  But even taken
together, they cannot prevent the existence of a large number of
software patents, and those patents will still cause serious problems.

Even if these measures cut the number of patents in half, that will
not change the situation very much.  A large computer system is likely
in the future to infringe many dozens of patents.  Half of that will
still be a large problem.

You can think of this as the equivalent of nuclear overkill.  How much
good does it do to block half (on the average) of the warheads in a
nuclear attack?  If the attack consists of a single warhead, this
could prevent all damage---a big improvement, though only 50%
probable.  If the attack consists of twenty warheads, blocking half
could do a great deal of good, even though the problem caused by the
remaining warheads would still be large.  If the attack consists of
1000 warheads, knocking out half of them will make little difference,
because the 500 remaining will destroy nearly everything.

There is no official figure for the number of software patents we have
today, but 4000 or 5000 is a likely estimate given past numbers and
trends.  There are 9000 applications in one category alone, so we can
expect to have many more software patents in the future.  To make
software development a safe activity again, we must do more than cut
the number of patents in half.  Eliminating 9/10 of them would be just
a start.